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Author Topic:   Convergent Evolution - Reasonable conclusion? or convenient excuse?
Percy
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Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 22 of 107 (564327)
06-09-2010 9:30 PM
Reply to: Message 18 by BobTHJ
06-09-2010 6:31 PM


What is the ID Explanation?
BobTHJ writes:
Not all traits fit neatly into a nested hierarchy.
It isn't traits that one places into a nested hierarchy but organisms, and organisms have many traits that must be considered collectively. Pretty much everyone is aware that lone traits can not be used to classify organisms. What sense would it make to classify dolphins and bats together on the basis of one gene and ignore the other tens of thousands of genes that not don't match and the many genes that don't even exist in both species. Under no circumstances would anyone ever group dolphins and bats together, not based on phenotypic evidence, and not based on genetic evidence.
The specific collection of traits of many organisms are sufficiently distinct that they can be classified with a high degree of confidence, but for other organisms classification can often be difficult, and then we must fall back on genetic analysis which is much more clear and much less ambiguous. With an extremely high level of confidence genetic analysis tells us the degree of relatedness of organisms and where they belong within the nested hierarchy. There can be no doubt that organisms fit within a nested hierarchy.
It is only because it is unusual that the Prestin gene has come to the attention of creationists. It represents a case of convergent evolution that shaped not only a protein in two different organisms to become more similar, but also the common gene that produces it. But as I told you in the other thread, and as WK has told you in this one, when you look at the DNA you see that the mutations don't match.
The nested hierarchy is just a natural result of imperfect reproduction for generation after generation, and natural selection is what drives organisms toward similar solutions for better reproductive success given similar environments. It accounts for organisms converging on similar solutions, like arctic rabbits and polar bears converging on the solution of white fur and heavier coats.
How does ID account for what we see genetically in cases of convergent evolution, where the phenotypic similarity is belied by a completely different genetic underpinning?
--Percy

This message is a reply to:
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Replies to this message:
 Message 39 by BobTHJ, posted 06-14-2010 5:15 PM Percy has replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 32 of 107 (564653)
06-11-2010 3:38 PM
Reply to: Message 31 by bluegenes
06-11-2010 3:27 PM


Also, brains use more resources per ounce than any other body part. The processing centers for echolocation are relatively substantial, and there would be high selection pressure against this allocation of resources unless its utility for the organism was very high.
AbE: I just discovered that bats (and maybe dolphins, too) have techniques they must employ to avoid deafening themselves when they emit echolocation sounds. Also, both predators and non-predators would find their survival chances negatively affected if their echolocation signals gave away their position, so even if echolocation provided them advantages in some respects, it would have disadvantages in others.
--Percy
Edited by Percy, : Add AbE.

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Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 33 of 107 (564657)
06-11-2010 3:51 PM
Reply to: Message 28 by BobTHJ
06-11-2010 12:30 PM


BobTHJ writes:
But consider that both classifications would also need to separately evolve enhanced cochlea and a high-frequency sound emission system and we're suddenly increasing the complexity and subsequent odds substantially...
What are the significant differences between a bat cochlea and, say, a human cochlea? What are the significant differences between bat vocalization and, say, human vocalization? Once you know the differences then you can better decide if any extraordinary difficulties would be involved in evolving them. My guess is that the differences are primarily shape, size, and (for the cochlea) number of hairs and the number of nerves traveling to the brain.
How would you compare the odds of a process that we have observed and that is known to produce the precise type of phenotypic and genetic evidence we observe, to the odds of a process that has never been observed and whose details are therefore completely unknown.
--Percy
Edited by Percy, : Grammar, improve clarity.

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Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 49 of 107 (565173)
06-15-2010 10:03 AM
Reply to: Message 39 by BobTHJ
06-14-2010 5:15 PM


Re: What is the ID Explanation?
BobTHJ writes:
Does ID have something to account for or explain? Convergence is a (potential) problem for common-ancestry evolution, not ID. The common Designer readily explains any convergence under ID.
Taq also replied to your message and asked a good question. Are both convergence and non-convergence evidence for ID? If so, can you explain?
But my question was about how the common Designer explains convergence. If humans are the model for how the Designer designs, as is often suggested, then what leads you to expect convergence since humans will not design from scratch but will reuse an existing design, if one is available.
Let's imagine that a human wanted to design an engine, but needed it to be more powerful than existing engines. He would take an existing design and modify it. But what if he didn't have an existing design. Maybe he wanted a Wankel engine, but he worked for Ford instead of Mazda, so he couldn't start with an existing design. In that case he would design from scratch.
Now let's consider the equivalent case for your designer. Let's say he wants an eye with some new feature, maybe greater resolution. If he designs like a human then he would modify an existing design. He would never have to design from scratch if there were prior designs, because the designer is the only company.
But the designer has obviously designed from scratch at least several times with the eye, and this tells us that there must have been several designers who were unwilling to share designs with one another. One designer designed the octopus eye and put the light rods in front of the blood supply, but then he wouldn't share that design with the designer of mammals, so that designer designed from scratch and put the rods in back of the blood supply.
What I just explained is what I was asking you about when I asked what convergent evolution tells us about the designer.
--Percy

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 Message 39 by BobTHJ, posted 06-14-2010 5:15 PM BobTHJ has replied

Replies to this message:
 Message 60 by BobTHJ, posted 06-16-2010 12:46 PM Percy has replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 51 of 107 (565185)
06-15-2010 11:46 AM
Reply to: Message 42 by BobTHJ
06-14-2010 6:10 PM


BobTHJ writes:
95%+ of organisms fit nicely into a nested hierarchy. However, the hierarchy can not fully model that last <5% because there will be shared features/genes with other not closely grouped organisms.
Can you provide an example or two of organisms in this last 5%?
And, though I've posted it elsewhere I'll restate it here for completeness: nested hierarchy does not imply common ancestry...
And though I've posted it elsewhere I'll restate it here because you haven't answered it yet: what else could a nested hierarchy possibly imply? How many trunks can a tree have?
--Percy

This message is a reply to:
 Message 42 by BobTHJ, posted 06-14-2010 6:10 PM BobTHJ has replied

Replies to this message:
 Message 61 by BobTHJ, posted 06-16-2010 1:02 PM Percy has replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 65 of 107 (565442)
06-16-2010 8:25 PM
Reply to: Message 60 by BobTHJ
06-16-2010 12:46 PM


Re: What is the ID Explanation?
Hi Bob,
So the question was, "How does the common designer explain convergence?" And I said that different designs for the same purpose indicate different designers. And you reply:
BobTHJ writes:
You're forgetting that design is purposeful. Yes there are several variations on the eye. This is because each differently designed eye serves a specific function to its host organism.
Sure, maybe each eye design had a different set of requirements that necessitated certain design choices. Or maybe there were different designers. How do you tell which it is? What evidence are you looking at that leads you to conclude a single designer?
--Percy

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Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 66 of 107 (565445)
06-16-2010 8:55 PM
Reply to: Message 61 by BobTHJ
06-16-2010 1:02 PM


BobTHJ writes:
quote:
Can you provide an example or two of organisms in this last 5%?
I already provided one. Bats and dolphins.
Genetically bats and dolphins fit neatly into the nested hierarchy. Your echolocation argument on the basis of a single gene out of tens of thousands was completely dismantled. The nucleotide sequences aren't the same, and the differences are the type produced by random mutation and selection converging on the same solution in separate lineages. It's a fascinating discovery that mutations that produced very similar proteins were selected for in both lineages, but they aren't the same mutations.
quote:
And though I've posted it elsewhere I'll restate it here because you haven't answered it yet: what else could a nested hierarchy possibly imply? How many trunks can a tree have?
A good ontological model. Yes, I have answered this before.
Sorry if I missed it, but if you could just provide a link to the message with this answer I'll go take a look. Otherwise, could you please answer the question? A nested hierarchy can, by definition, have but a single root node. The phenotypic evidence strongly indicates a nested hierarchy, as was obvious even before Darwin, and the genetic evidence proves it conclusively.
--Percy

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Percy
Member
Posts: 22388
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:
 Message 81 by Dr Jack, posted 06-22-2010 9:15 AM Percy has replied
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Percy
Member
Posts: 22388
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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Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 91 of 107 (566123)
06-23-2010 5:46 AM
Reply to: Message 90 by Dr Jack
06-23-2010 5:06 AM


Re: Tree Lengths
Hi all,
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?
The performance of the PARS program is a consideration. If I ended up with final population sizes of a billion individuals with genome sizes of a billion nucleotides I assume the PARS program would never finish. What would be a reasonable genome size and a reasonable final population size? Now that I think about this, I think I'll need to have random death and a fixed maximum population size. If all individuals always reproduce and all offspring always live the tree would grow too big.
And most importantly, predictions. What do we predict we should see from the PARS program for both cases? In other words, if I handed you sets of genomes of the individuals of final populations, one set each for both standard evolution and design, would you be able to tell which was which from the PARS analysis? I'm challenging you (or WK or someone) to develop the criteria for telling the difference. Then I will provide you the genomes for 100 final populations. Half will be evolution, half will be design, and you have to figure out which is which. If your criteria are unable to distinguish then you'll get roughly 50% correct. If your criteria are perfect then you'll get 100% correct. What do you think is a reasonable criteria that would demonstrate that the PARS program can tell the difference between populations that developed solely through descent versus from a set of originally designed individuals.
--Percy

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