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Author Topic:   Convergent Evolution - Reasonable conclusion? or convenient excuse?
bluescat48
Member (Idle past 4189 days)
Posts: 2347
From: United States
Joined: 10-06-2007


Message 76 of 107 (565876)
06-21-2010 5:59 PM
Reply to: Message 71 by BobTHJ
06-21-2010 4:57 PM


As previously stated, if there were no common designer then we could expect to see little to no similarity between organisms.
Why? If evolution is correct then one would see similarities. The lack of similarities would be evidence that there was a designer. The similarities show descent. Similarities among non closely related species still show descent, but from a different start point.

There is no better love between 2 people than mutual respect for each other WT Young, 2002
Who gave anyone the authority to call me an authority on anything. WT Young, 1969
Since Evolution is only ~90% correct it should be thrown out and replaced by Creation which has even a lower % of correctness. W T Young, 2008

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articulett
Member (Idle past 3371 days)
Posts: 49
Joined: 06-15-2010


Message 77 of 107 (565877)
06-21-2010 5:59 PM
Reply to: Message 71 by BobTHJ
06-21-2010 4:57 PM


quote:
Kludgey? Care to give an example of kludgey? YEC does expect some degree of 'kludgeyness' as a result of decay in the genome since creation - but this type of kludgeyness should be as a result of degredation - not as a result of natural selection's imperfect means of assembling functions.
http://onegoodmove.org/...ve/2010/06/richard_dawkins_21.html
quote:
As previously stated, if there were no common designer then we could expect to see little to no similarity between organisms. Each would have different "building blocks" - they wouldn't share common cellular structure, DNA, etc.
Yes, but why does an elephant look more like a mammoth than a pig? Why can every school child tell that a cat is more related to a lion then it is to a dog? When did such critters last share a common ancestor? Why psueudogenes that worked in primitive ancestors but not in current owners? Why ERV's? Etc. Or is that all part of god's unexplained mystery to you --stuff that can't be known?
quote:
At this point I am doubtful that scientific evidence alone could convince me of the lack of a designer - I am convinced by the spiritual evidence. However, scientific evidence could convince me that the designer used darwinian evolution as a method for populating life on the planet. As to what form that evidence would take - I am uncertain - I honestly haven't given it much thought.
Obviously. I think creationists are even afraid to consider they might be wrong; whereas, science is all about trying to prove a theory wrong, because that is the best way to find out what is right. If you don't know what you'd expect find in an evolved world versus what you'd expect to find in a world specially created 6000 years ago, how do you have any possible way of evaluating one claim over the other? The former has confirming evidence in every major scientific field. The latter has an old book of supposed divine truths that are often contradictory and don't serve to further ANY scientific understanding of anything.
How do you know you are not being fooled the same way these people are being fooled? https://www.youtube.com/watch?v=q7BQKu0YP8Y , and would you want to know if you were?
To me your beliefs are as sincere but as delusional as theirs and you have left yourself no means of discovering this. Moreover, these beliefs prevent you from understanding the facts. I think it's too late to try to talk logically with some people. Some people become "addicted" to their delusions.

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RAZD
Member (Idle past 1405 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
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 79 of 107 (565881)
06-21-2010 7:09 PM
Reply to: Message 75 by Dr Adequate
06-21-2010 5:57 PM


Nostalgia
Man! Professor Branestawm, that takes me back.
TTFN,
WK

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Percy
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Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 80 of 107 (565962)
06-22-2010 8:49 AM
Reply to: Message 70 by BobTHJ
06-21-2010 4:39 PM


The Designer Designed in a Nested Hierarchy
BobTHJ writes:
There are a lot of assumptions made to force the ontology to fit the nested-heirarchy "root node" model needed for common ancestry. Here's where the system seems to break down. While a "best guess" path has been established it requires a lot of faith in processes supposed to occur millions or billions of years in the past for which there is scant evidence. I'm happy to discuss aspects of this further if you deem it to be adequately on-topic.
I thought you said you answered this already and were just going to tell me which post the answer was in?
Anyway, let me illustrate what you're actually up against in trying to disprove a nested hierarchy with a very simple example. It has to be bery simple otherwise it doesn't fit in a message and wouldn't be easily understood, but the principles are the same.
Take a very simple genome with the letters A through G. We start with a single organism with a seven letter genome: AAAAAAA. We follow the organism's evolution through three succeeding generations where there are just two offspring per generation, and each offspring experiences one and only one random mutation, no more, no less. Here's the tree I get using a simple Perl program to give me random positions and letters for the mutations:
AAAAAAA
                      _____________|_______________
                     /                             \
              AAAAABA                               AAAEAAA
             ____|____                           ______|___
            /         \                         /          \
     AAAAAGA           GAAAABA           AAAGAAA            AAAEABA
       _|_               _|_               _|_                _|_
      /   \             /   \             /   \              /   \
AFAAAGA  AAAAAGC  GAAGABA  GAEAABA   AAAGAEA  AAEGAAA   AAAEAEA  AAAEGBA
That last row is analogous to life we see on earth today. We don't have the genomes of past organisms available to us, only today's (actually, we do have the DNA of some past organisms, but this example doesn't include that possibility). So the genomes of our 8 descendent organisms are:
  1. AFAAAGA
  2. AAAAAGC
  3. GAAGABA
  4. GAEAABA
  5. AAAGAEA
  6. AAEGAAA
  7. AAAEAEA
  8. AAAEGBA
Here are 8 randomly generated genomes:
  1. FDDCEBG
  2. ADAGGDG
  3. EBDCCCE
  4. FAAGGDA
  5. FBFGGBF
  6. ECEEBBB
  7. EGGAAEE
  8. CFCGAEE
The first list of the results of three generations of descent fits in a nested hierarchy. It's simple enough that you could reconstruct the genealogy chart with just that list working by hand. The second list cannot be placed in a nested hierarchy, no matter how hard you try.
There are computer programs that do this for you (I don't happen to have one myself, maybe WK knows of one we could get) that could demonstrate this for you unequivocally.
Bottom line: The genomes of current species fit in a nested hierarchy. If a designer created existing life then he designed in a nested hierarchy. But there's no evidence for a designer, and a nested hierarchy is what is produced by the normal kind of reproduction we observe occurring in all life today.
--Percy

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Replies to this message:
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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 81 of 107 (565965)
06-22-2010 9:15 AM
Reply to: Message 80 by Percy
06-22-2010 8:49 AM


Re: The Designer Designed in a Nested Hierarchy
I ran both of your examples through PARS and it gave these trees:
For your nested version, it finds a single tree of tree length 12:
+--------Taxon 8
           +--------6
           |        |        +Taxon 7
           |        +--------5
           |                 |        +----------------Taxon 6
  +--------3                 +--------4
  |        |                          +Taxon 5
  |        |
  |        |        +--------Taxon 4
  |        +--------2
  |                 +--------Taxon 3
  |
  1--------Taxon 2
  |
  +--------Taxon 1
Unfortunately, PARS requires an outgroup to work best and treats the first taxon as the outgroup if it doesn't get one so this is a bit off, but note that even so it has grouped most of the final pairings together and identified taxons 7&8 and 5&6 as more closely related to each other than to any other taxon.
Now if we look at the random sequences, two most parsimonious trees are found, both with tree length 28:
+---------Taxon 5
            |
  +---------3            +-------------------------Taxon 6
  |         |            |
  |         +------------4             +-----------------Taxon 8
  |                      |             |
  |                      +-------------5-----------------Taxon 7
  |                                    |
  |                                    +-----------------Taxon 3
  |
  |           +-----------Taxon 4
  1-----------2
  |           +-----Taxon 2
  |
  +-----------Taxon 1
and
+---------Taxon 5
            |
            |                                 +-------------Taxon 8
  +---------3              +------------------5
  |         |              |                  +-------------Taxon 7
  |         |              |
  |         +--------------4----------------------------Taxon 6
  |                        |
  |                        +----------------Taxon 3
  |
  |           +-----------Taxon 4
  1-----------2
  |           +-----Taxon 2
  |
  +-----------Taxon 1
To be honest, I'm pretty surprised at how nested that came out.
(edit) Actually, when I think about it, I'm not. If you think about it there are only 7 characters, so the maximum possible tree length is going to 49*. So that a random set produces an intermediate value kind of makes sense. There are a bunch of long arms in that "tree".
* - Actually that's an overestimate because there are only 6 states for each character but I can't think what that makes it off the top of my head.
Edited by Mr Jack, : No reason given.
Edited by Mr Jack, : No reason given.

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Replies to this message:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 82 of 107 (565970)
06-22-2010 9:34 AM
Reply to: Message 80 by Percy
06-22-2010 8:49 AM


Re: The Designer Designed in a Nested Hierarchy
The second list cannot be placed in a nested hierarchy, no matter how hard you try.
I'm with Mr. Jack on this one, I don't see why you couldn't put those into a nested hierarchy. I was planning to run your examples through some of the PHYLIP programs myself but Mr. Jack saved me the bother.
That said I think it would be interesting to see what happens if Jack runs those two sets of data through the seqboot program first to produce a bootstrap analysis. The real distinction between genuine sequences and randomly generated ones is not tha ability to order them in a nested hierarchy but the ability to do so in such a way that they are significantly distinct from the results one would get from ordering random sequences in a nested hierarchy.
So I would predict that for a set of genuine homolgous DNA sequences against a set of randomly generated sequences you would get a well supported tree for the genuine sequences and a very poorly supported tree for the random ones. As far as your examples go, I'm not sure how those would fare in such an analysis since they need to be analysed as characteristics rather than as sequence data. I think the tree length distances Mr. Jack notes are also an important distinction.
TTFN,
WK
Edited by Wounded King, : misspelling of fare

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Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 83 of 107 (565976)
06-22-2010 9:48 AM
Reply to: Message 81 by Dr Jack
06-22-2010 9:15 AM


Re: The Designer Designed in a Nested Hierarchy
Hi Mr Jack!
This is great. PARS is one of the programs I saw referenced when I tried to look this up, but the blurb about it mentioned an outgroup, and I wasn't sure what I should do if I didn't have one.
What does "tree length" mean?
Even while I was writing that post it occurred to me that with a genome of size 7 that any decent program should be able to fit the random genomes into a nested hierarchy, that the likelihood of internal contradictions preventing it might be unlikely at that size. But might the possibility of internal contradictions be impossible at any size? Perhaps random genomes of any size could be fit into nested hierarchies by a good program. If so then Bob is correct that the ability to place genomes into a nested hierarchy is not evidence that those genomes were the result of normal reproduction.
Is there a good place to pick up the PARS program? Did you have to fiddle with the output, or did it just give you those trees as is. If I find some time I could play around with it.
--Percy

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Replies to this message:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 84 of 107 (565979)
06-22-2010 10:05 AM
Reply to: Message 83 by Percy
06-22-2010 9:48 AM


Re: The Designer Designed in a Nested Hierarchy
Hi Percy I just ran the program using the input file ...
8 7
AFAAAGA AFAAAGA
AAAAAGC AAAAAGC
GAAGABA GAAGABA
GAEAABA GAEAABA
AAAGAEA AAAGAEA
AAEGAAA AAEGAAA
AAAEAEA AAAEAEA
AAAEGBA AAAEGBA
And got the same tree as Mr. Jack.
+--------AAAEGBA
           +--------6
           |        |        +AAAEAEA
           |        +--------5
           |                 |        +----------------AAEGAAA
  +--------3                 +--------4
  |        |                          +AAAGAEA
  |        |
  |        |        +--------GAEAABA
  |        +--------2
  |                 +--------GAAGABA
  |
  1--------AAAAAGC
  |
  +--------AFAAAGA
You can get the Pars program along with the rest of the PHYLIP package at the link in Message 82.
I tried bootstrapping that first set of data and got this ...
+-------AFAAAGA
                          +--64.0-|
                          |       +-------AAAAAGC
                  +--19.6-|
                  |       |       +-------GAAGABA
                  |       +--42.4-|
          +--32.6-|               +-------GAEAABA
          |       |
          |       |               +-------AAAGAEA
  +-------|       +----------20.7-|
  |       |                       +-------AAEGAAA
  |       |
  |       +-------------------------------AAAEAEA
  |
  +---------------------------------------AAAEGBA
Where the branch numbers represent how many time out of 100 those particular groupings came out in the bootstrapping.
Sadly for your argument Percy the bootstrapping of the random data sets actually gives an arguably more robust hierarchy in that most of the branches are better supported.
+-------ADAGGDG
                                          +--80.7-|
                                  +--46.6-|       +-------FAAGGDA
                                  |       |
                          +--56.9-|       +---------------FDDCEBG
                          |       |
                  +--28.1-|       +-----------------------FBFGGBF
                  |       |
          +--50.6-|       +-------------------------------ECEEBBB
          |       |
  +-------|       +---------------------------------------EBDCCCE
  |       |
  |       +-----------------------------------------------EGGAAEE
  |
  +-------------------------------------------------------CFCGAEE
I think what this really shows is that 7 characteristics is a very small sample to draw any sort of conclusion from.
TTFN,
WK
Edited by Wounded King, : Added bootstrapped tree.
Edited by Wounded King, : Added bootstrapped tree of random data sets.
Edited by Wounded King, : Because I can't tell the difference between 7 and 8, that'll teach me to try arithmetic without using my fingers.

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 85 of 107 (565986)
06-22-2010 10:30 AM
Reply to: Message 83 by Percy
06-22-2010 9:48 AM


Re: The Designer Designed in a Nested Hierarchy
Hi Percy,
This is great. PARS is one of the programs I saw referenced when I tried to look this up, but the blurb about it mentioned an outgroup, and I wasn't sure what I should do if I didn't have one.
It can work by treating one of the taxons as the outgroup (taxon 1, here). The analysis will then be less good at determining the rooting of the tree - as, in fact, we see - since it doesn't know which states are primitive (unchanged from the ancestral species) and which are derived (changed from the ancestral species).
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.
Perhaps random genomes of any size could be fit into nested hierarchies by a good program. If so then Bob is correct that the ability to place genomes into a nested hierarchy is not evidence that those genomes were the result of normal reproduction.
If you start with the assumption of a nested tree, you can fit data to it. What will be different is the nature of that tree, and the length of that tree, I'd guess. You'd also expect to have more different most parsimonious trees, I think.
Is there a good place to pick up the PARS program? Did you have to fiddle with the output, or did it just give you those trees as is. If I find some time I could play around with it.
Er, I got it with my course materials, I assume Wounded King's link will take you to where you can get it. I needed to tweak a couple of settings to produce the correct formation of the output, but I didn't post-process it at all or make any attempt to alter the trees (although I did cut those trees out of a more detailed output).

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 86 of 107 (565991)
06-22-2010 10:44 AM
Reply to: Message 80 by Percy
06-22-2010 8:49 AM


Re: The Designer Designed in a Nested Hierarchy
Here are 8 randomly generated genomes:
  1. FDDCEBG
  2. ADAGGDG
  3. EBDCCCE
  4. FAAGGDA
  5. FBFGGBF
  6. ECEEBBB
  7. EGGAAEE
  8. CFCGAEE
For arguments sake, if these were separately created organisms then you could also have the following list:
  1. FDDCEBG
  2. XXYYYYYY
  3. 1244434
  4. URRWWVR
  5. and so on, with no shared genetic systems

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 87 of 107 (565993)
06-22-2010 10:47 AM
Reply to: Message 75 by Dr Adequate
06-21-2010 5:57 PM


But what it could not do is unhook our nerves from the back of the retina, re-attach them to the front of our retina, giving us a blind spot, and then rewire our brains so as to automatically fill in the blind spot with a best guess.
Not only that, but this same deteriotation has to occur in all animals that have a backbone during the same time period.

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RAZD
Member (Idle past 1405 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
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) • • •

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 89 of 107 (566112)
06-23-2010 4:11 AM
Reply to: Message 88 by RAZD
06-22-2010 10:20 PM


Re: Tree Lengths
Doesn't Percy's original tree only have a length of 3?
No, because the length is cumulative for all branches so I make Percy's tree out as having a length of 14. Also Percy's tree has a quite different topology because he has an ancestral sequence making it a rooted tree. The Pars program also doesn't correct for multiple changes overlaying each other, so the 2 changes at position 4 will confound it.
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.
+AAAAAAA
  |
  3-----------------------AAEGAAA
  |
  |           +-----------------------AAAGAEA
  |           |
  |           |                       +-----------AAAEGBA
  |           |           +-----------5
  |           |           |           +-----------AAAEAEA
  +-----------1-----------4
              |           |           +-----------GAEAABA
              |           +-----------2
              |                       +-----------GAAGABA
              |
              +-----------AAAAAGC
              |
              +-----------AFAAAGA   
Another big difference is that the Pars program cannot be contrained with Percy's 1 step mutation condition.
Running it with slightly diffferent variables the program actually produces an alternative rooted tree with a tree length of only 13.
+AAAAAAA
  |
  4-----------------------AAEGAAA
  |
  |                       +-----------AAAEGBA
  |           +-----------6
  |           |           |           +AAAEAEA
  |           |           +-----------5
  |           |                       +-----------AAAGAEA
  |           |
  |           |           +-----------GAEAABA
  +-----------2-----------3
              |           +-----------GAAGABA
              |
              |           +-----------AAAAAGC
              +-----------1
                          +-----------AFAAAGA 
The program also produces a table which lets us see what ancestral states it has inferred.
From    To     Any Steps?    State at upper node
                             ( . means same as in the node below it on tree)

root      4                AAAAAAA
   4   AAAAAAA      no     .......
   4   AAEGAAA      yes    ..EG...
   4      2         yes    .....B.
   2      6         yes    ...E...
   6   AAAEGBA      yes    ....G..
   6      5         yes    .....E.
   5   AAAEAEA      no     .......
   5   AAAGAEA      yes    ...G...
   2      3         yes    G......
   3   GAEAABA      yes    ..E....
   3   GAAGABA      yes    ...G...
   2      1         yes    .....G.
   1   AAAAAGC      yes    ......C
   1   AFAAAGA      yes    .F.....
TTFN,
WK
Edited by Wounded King, : No reason given.

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 90 of 107 (566119)
06-23-2010 5:06 AM
Reply to: Message 88 by RAZD
06-22-2010 10:20 PM


Re: Tree Lengths
Hi RAZD,
I'm curious why the original tree was not reproduced by this analysis. Certainly it should be the most parsimonious solution, yes?
I'm curious too The first reason I can see is that there's no outgroup, although, as Wounded as already shown, even that doesn't help much. 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). Because this was the only mutation in that branch, the information needed to group the later pairings together has been completely lost. The same has happened on the righthand branch (AAAEAAA->AAAGAAA).
In real data, there'd be many more datapoints, and more states; usually allowing multiple changes in the same character to the be resolved.

This message is a reply to:
 Message 88 by RAZD, posted 06-22-2010 10:20 PM RAZD has seen this message but not replied

Replies to this message:
 Message 91 by Percy, posted 06-23-2010 5:46 AM Dr Jack has not replied
 Message 92 by bluegenes, posted 06-23-2010 6:04 AM Dr Jack has not replied

  
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