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Author Topic:   Twin-Nested Heirarchy
Chiroptera
Member
Posts: 6531
From: Oklahoma
Joined: 09-28-2003


Message 31 of 49 (430965)
10-28-2007 3:36 PM
Reply to: Message 29 by Dr Adequate
10-28-2007 2:30 PM


I just looked at mark's post, the one that started this:

And yet a tortoise has more similar sequences to a bird than a small mammal with a high metabolism.

Since most people think that the synapsids (mammals) split from the diapsids/anapsids (birds and tortoises) before anapsids and diapsids split, then marks point is valid: we would expect that warm-blooded birds would share more molecular similarities to cold-blooded tortoises than to warm-blooded mammals.


Computers have cut-and-paste functions. So does right-wing historical memory. -- Rick Perlstein
This message is a reply to:
 Message 29 by Dr Adequate, posted 10-28-2007 2:30 PM Dr Adequate has not yet responded

  
Doddy
Member (Idle past 4013 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 32 of 49 (431007)
10-28-2007 8:00 PM
Reply to: Message 27 by crashfrog
10-28-2007 11:46 AM


crashfrog writes:

What's your evidence for that? And are you aware that this is a dodge?

Clearly, a change within a lice genus is much simpler and more straigthfoward to compare than, say, mice and men.

crashfrog writes:

I've given you ample reason to believe me - the topological convergence of phylogenies we've been talking about. It settled the issue two pages ago but you don't seem to get that, yet.


But how does convergence of a set of results immediately prove all results collected by that method?

crashfrog writes:

You haven't presented any such evidence, because the papers you're presenting aren't talking about introns.


*Sigh* Perhaps I should be more specific. Instead of citing reviews and opinion pieces (which in and of themselves, contain no evidence) to give you a broad overview, how about a research article:

Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. "The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila." Cell. 130(1):89-100 (2007 Jul 13)


Help to inform the public - contribute to the EvoWiki today!

This is what we are up against. There are thousands around the world more being (home-)schooled in the same way. But the internet is far reaching! Teach evolution by joining the Evolution Education Wiki today!


This message is a reply to:
 Message 27 by crashfrog, posted 10-28-2007 11:46 AM crashfrog has responded

Replies to this message:
 Message 33 by crashfrog, posted 10-28-2007 9:08 PM Doddy has responded
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crashfrog
Inactive Member


Message 33 of 49 (431027)
10-28-2007 9:08 PM
Reply to: Message 32 by Doddy
10-28-2007 8:00 PM


But how does convergence of a set of results immediately prove all results collected by that method?

The same way that calibrating a scale to a known weight confirms its ability to measure other weights, as I explained. Are you going to ape creationist to the extent of asking questions already answered? (It would be nice if creationists could be shown how to address the arguments of evolutionists honestly, instead of with a never-ending series of dodges.)

Instead of citing reviews and opinion pieces (which in and of themselves, contain no evidence) to give you a broad overview, how about a research article:

How about a research article that's actually relevant? We're not doing phylogeny on "mirtrons" or short introns, they're too short. Indeed most of the phylogeny we're doing is based on mitochondrial sequences, not nuclear sequences, with lots of repetition (to generate sufficiently long sequences when restricted.)


This message is a reply to:
 Message 32 by Doddy, posted 10-28-2007 8:00 PM Doddy has responded

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Doddy
Member (Idle past 4013 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 34 of 49 (431066)
10-29-2007 2:56 AM
Reply to: Message 33 by crashfrog
10-28-2007 9:08 PM


crashfrog writes:

The same way that calibrating a scale to a known weight confirms its ability to measure other weights, as I explained.


And, as I said, you can't measure ship tonnage with a scale calibrated with a 100g weight.

You asked why I think that gophers are more simple than any other species complex. I don't think that. I think that other species complexes are probably fairly similar. If the gophers and lice are at 100g, then the other species complexes will be in the range of 20-300g.

But to be able to use the same techniques on a much broader scale, say at the level of the family or order, is going beyond what has been calibrated. One can't say that because we can accurately construct a phylogeny for various species of gophers, that we can also construct one for various orders of eutherian mammals. That's extrapolating too far for creationist me. You're going to have to show that it works at the level of tonnage.


Help to inform the public - contribute to the EvoWiki today!

This is what we are up against. There are thousands around the world more being (home-)schooled in the same way. But the internet is far reaching! Teach evolution by joining the Evolution Education Wiki today!


This message is a reply to:
 Message 33 by crashfrog, posted 10-28-2007 9:08 PM crashfrog has not yet responded

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Rrhain
Member
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 35 of 49 (431068)
10-29-2007 3:16 AM
Reply to: Message 1 by Doddy
10-25-2007 12:03 AM


Goddy writes:

quote:
But what they (the evilutionists) don't tell you is that similarities are not evidence of common descent. They can also be indicators of common design.

Except the history of eyes proves this to be wrong.

Vision seems to have evolved about 40 times in the history of life on earth. Take a look at the eye of the cephalopod and the eye of the primate.

Primate retinas are inside-out. In primates, the nerves that connect the photosensitive cells to the optic nerve run in front of those very photosensitive cells. This means that photons must penetrate the nerve tissue in order to reach the photosensitive cells, thus resulting in a loss of visual acuity.

Plus, this means that the nerves must eventually pierce the photosensitive tissue at some point in order to have the optic nerve reach the brain, thus there necessarily is a blind spot in the eye and again, a loss of visual acuity.

Cephalopod eyes, however, don't have these problems as the nerve tissue is behind the photosensitive cells.

So if there were a designer and if this designer were to use similar designs, why is there a difference between primate and cephalopod eyes? Shouldn't vision be identical across species?

Instead, this can only be rectified by an evolutionary process. The congruence of morphology and genetics show an evolutionary pattern, not a designed pattern.


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.
This message is a reply to:
 Message 1 by Doddy, posted 10-25-2007 12:03 AM Doddy has responded

Replies to this message:
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Rrhain
Member
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 36 of 49 (431069)
10-29-2007 3:25 AM
Reply to: Message 32 by Doddy
10-28-2007 8:00 PM


Goddy writes:

quote:
Clearly, a change within a lice genus is much simpler and more straigthfoward to compare than, say, mice and men.

I don't think you understand the point of the example. This is also justified by your previous claim of, "They're still gophers and lice."

Nobody is trying to say that the lice evolved into gophers or vice versa.

What they are saying is that the evolutionary history of the lice is necessarily dependent upon the evolutionary history of the gophers. As was pointed out, the lice only mate when the gophers do. If the gophers experience a speciation even such that what was once a single population of mating gophers now becomes two exclusive populations of mating gophers, then the lice are also necessarily separated.

With no gene flow between the lice in the two isolated gopher populations, they will necessarily follow different evolutionary paths.

This makes no sense from a design point of view. Using the morphology of the lice, you can develop a timeline of when they speciated. And sure enough, that history matches exactly the speciation history of the gophers.

The gene changes match the morphology changes.

And to answer the underlying insinuation: Of course they're still lice and gophers. But they're a new kind of lice and gopher.

quote:
But how does convergence of a set of results immediately prove all results collected by that method?

Huh? Do you not understand what "convergence" means? You're asking why the showing of a circle to be round proves that it actually is round. Unless you're trying to say that there's no such thing as a circle to begin with....


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.
This message is a reply to:
 Message 32 by Doddy, posted 10-28-2007 8:00 PM Doddy has not yet responded

    
Rrhain
Member
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 37 of 49 (431070)
10-29-2007 3:34 AM
Reply to: Message 34 by Doddy
10-29-2007 2:56 AM


Goddy writes:

quote:
And, as I said, you can't measure ship tonnage with a scale calibrated with a 100g weight.

You can if it's sufficiently sensitive and functional across the expected weight range. Do you have evidence that it isn't?

quote:
If the gophers and lice are at 100g, then the other species complexes will be in the range of 20-300g.

Again with the implication that somehow lice evolved into gophers. Nobody is saying that. Instead, they're saying that the lice necessarily speciate in time with the gophers precisely because the only time the lice can mate is when the gophers mate.

If the gophers speciate and thus create two isolated populations, then the lice those gophers carry necessarily become isolated and will therefore follow different evolutionary paths.

If you follow the morphology of the lice, you find the speciation pattern of the gophers. That's something that's only explainable via evolutionary methods, not design.

quote:
But to be able to use the same techniques on a much broader scale, say at the level of the family or order, is going beyond what has been calibrated.

Why? You seem to think that you can find an individual organism that is a representative sample of a "family" or "order." You can't. Every single organism is a member of a species. Every organism is just as evolved as every other organism. It isn't like billions of years ago there was an "animal" and a "plant" and a "fungus" and a "monera." Instead, there were species.

There are always species.

quote:
One can't say that because we can accurately construct a phylogeny for various species of gophers, that we can also construct one for various orders of eutherian mammals.

Why not? What's different about the other mammals that makes them so different from these? What is it about the process of examining morphology that is effective in one scenario but not another?

Be specific.

quote:
You're going to have to show that it works at the level of tonnage.

We have.

Why do you not accept it?

Be specific.


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.
This message is a reply to:
 Message 34 by Doddy, posted 10-29-2007 2:56 AM Doddy has responded

Replies to this message:
 Message 39 by Doddy, posted 10-29-2007 8:51 AM Rrhain has responded

    
Doddy
Member (Idle past 4013 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 38 of 49 (431087)
10-29-2007 8:32 AM
Reply to: Message 35 by Rrhain
10-29-2007 3:16 AM


Rrhain writes:

So if there were a designer and if this designer were to use similar designs, why is there a difference between primate and cephalopod eyes?


Who says that the designer would always want to use similar designs? We can't know the mind of the designer. Perhaps there is a very good reason for this design, but we might not know it yet.

Edited by Goddy, : clarify


Help to inform the public - contribute to the EvoWiki today!

This is what we are up against. There are thousands around the world more being (home-)schooled in the same way. But the internet is far reaching! Teach evolution by joining the Evolution Education Wiki today!


This message is a reply to:
 Message 35 by Rrhain, posted 10-29-2007 3:16 AM Rrhain has not yet responded

    
Doddy
Member (Idle past 4013 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 39 of 49 (431091)
10-29-2007 8:51 AM
Reply to: Message 37 by Rrhain
10-29-2007 3:34 AM


Rrhain writes:

You can if it's sufficiently sensitive and functional across the expected weight range. Do you have evidence that it isn't?


So, you are just assuming that all life evolved from a common ancestor to do some cladistics that allegedly is evidence of exactly what you assumed to begin with.

Rrhain writes:

Again with the implication that somehow lice evolved into gophers. Nobody is saying that.


Yep, not even me.

Rrhain writes:

If you follow the morphology of the lice, you find the speciation pattern of the gophers. That's something that's only explainable via evolutionary methods, not design.


Never said that was design. Enough with the strawmen already.

Rrhain writes:

There are always species.


Never said there wasn't. Just said that you can't use a method that is known to work on the genus level and expect it will work on the order level, say constructing a phylogenetic tree containing mice and men.

Rrhain writes:

Why do you not accept it?


When you say:

If we are correct in our assumption that all life is commonly descended, our cladistic analysis will be correct. Therefore, life was all descended from a common ancestor.

And expect me to believe you, I have to disagree. At worst, you are begging the question. At best, you are affirming the consequent. Choose your fallacy.


Help to inform the public - contribute to the EvoWiki today!

This is what we are up against. There are thousands around the world more being (home-)schooled in the same way. But the internet is far reaching! Teach evolution by joining the Evolution Education Wiki today!


This message is a reply to:
 Message 37 by Rrhain, posted 10-29-2007 3:34 AM Rrhain has responded

Replies to this message:
 Message 40 by crashfrog, posted 10-29-2007 9:52 AM Doddy has responded
 Message 41 by Wounded King, posted 10-29-2007 5:04 PM Doddy has not yet responded
 Message 44 by Rrhain, posted 10-30-2007 3:50 AM Doddy has not yet responded

    
crashfrog
Inactive Member


Message 40 of 49 (431105)
10-29-2007 9:52 AM
Reply to: Message 39 by Doddy
10-29-2007 8:51 AM


Just said that you can't use a method that is known to work on the genus level and expect it will work on the order level, say constructing a phylogenetic tree containing mice and men.

Why not, if it's species to species at every step?


This message is a reply to:
 Message 39 by Doddy, posted 10-29-2007 8:51 AM Doddy has responded

Replies to this message:
 Message 42 by Doddy, posted 10-29-2007 8:04 PM crashfrog has responded

  
Wounded King
Member (Idle past 2198 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 41 of 49 (431164)
10-29-2007 5:04 PM
Reply to: Message 39 by Doddy
10-29-2007 8:51 AM


Never said there wasn't. Just said that you can't use a method that is known to work on the genus level and expect it will work on the order level, say constructing a phylogenetic tree containing mice and men.

But it does work for that, very well. The literature is full of phylogenetic trees encompassing mice and men, not to mention worms, flies, frogs, jellyfish and all sorts of other animals. I could whip you one up myself if you like.

TTFN,

WK


This message is a reply to:
 Message 39 by Doddy, posted 10-29-2007 8:51 AM Doddy has not yet responded

    
Doddy
Member (Idle past 4013 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 42 of 49 (431195)
10-29-2007 8:04 PM
Reply to: Message 40 by crashfrog
10-29-2007 9:52 AM


crashfrog writes:

Why not, if it's species to species at every step?


Because I'm going to draw a completely arbitrary line in the sand where you implicate that evolution between kinds can occur, therefore showing a relationship between humans and chimps. Or, because I'll adhere to the bronze age belief that the world is only 6000 years old, and that no amount of evolution could do such things.

I don't know...I give up. If I continue, I risk ending up like the creo in my avatar.

I'd like to thank crashfrog, Mr A, bluegenes and mark24 for making some great posts in this thread. You've been very helpful for me in writing the EvoWiki page on Nested Hierarchy.

I'd also like to thank Ashby Camp from TrueOrigins for his creationist material: A Critique of Douglas Theobald’s “29 Evidences for Macroevolution”: “One True Phylogenetic Tree”.


Help to inform the public - contribute to the EvoWiki today!

This is what we are up against. There are thousands around the world more being (home-)schooled in the same way. But the internet is far reaching! Teach evolution by joining the Evolution Education Wiki today!


This message is a reply to:
 Message 40 by crashfrog, posted 10-29-2007 9:52 AM crashfrog has responded

Replies to this message:
 Message 43 by crashfrog, posted 10-29-2007 11:18 PM Doddy has not yet responded
 Message 45 by Rrhain, posted 10-30-2007 4:00 AM Doddy has not yet responded
 Message 46 by Dr Adequate, posted 10-30-2007 4:12 AM Doddy has responded

    
crashfrog
Inactive Member


Message 43 of 49 (431224)
10-29-2007 11:18 PM
Reply to: Message 42 by Doddy
10-29-2007 8:04 PM


I'd like to thank crashfrog, Mr A, bluegenes and mark24 for making some great posts in this thread. You've been very helpful for me in writing the EvoWiki page on Nested Hierarchy.

I hope you'll feel free to quote or paraphrase anything I've said, even without attribution.

Good show, though. Well done.


This message is a reply to:
 Message 42 by Doddy, posted 10-29-2007 8:04 PM Doddy has not yet responded

  
Rrhain
Member
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 44 of 49 (431239)
10-30-2007 3:50 AM
Reply to: Message 39 by Doddy
10-29-2007 8:51 AM


Doddy responds to me:

quote:
So, you are just assuming that all life evolved from a common ancestor to do some cladistics that allegedly is evidence of exactly what you assumed to begin with.

I understood every word in that sentence, but the sentence makes no sense.

No, we are not assuming anything. We are concluding it. The reason we conclude common ancestry is because the morphological evidence and the genetic evidence, which are independent, match up so precisely. There's no reason why they should if there were no common descent. Since they do, we conclude common descent.

quote:
Just said that you can't use a method that is known to work on the genus level and expect it will work on the order level, say constructing a phylogenetic tree containing mice and men.

Huh? You're not about to invoke "microevolution" and "macroevolution," are you? As if there were any difference between the two. "Macroevolution" is simply evolutionary methods that happen above the species level while "microevolution" are the exact same methods but taking place below. In other words, "macroevolution" is nothing more than a bunch of "microevolution."

If 1 + 1 = 2, why can't 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 = 10?

Hint: Everything is a species. When we talk about "above the species level," we mean that the speciation events that split one species into many are so diverse and significant as to be logically described by another cladistic group.

I am not my cousin. My cousin is not me. I am not descended from my cousin. My cousin is not descended from me. Instead, we have a common ancestor who is neither me nor my cousin: Our grandparents.

That doesn't mean that me, my cousin, or our grandparents were some nebulous form. We were each as highly developed as the rest of us. But because my cousin and are so close and share such a recent common ancestor, we're not that far apart.

But that's only because it's my first cousin. My seventh and eight cousins, however, are very distinct from me and that's because our common ancestor was much more distant.

And yet...every single individual in this tree is just as developed as every other.

Surely you can see why this is so. Let's not be disingenuous and claim, "But they're all people!" Surely you can perform the abstraction.

quote:
If we are correct in our assumption that all life is commonly descended, our cladistic analysis will be correct. Therefore, life was all descended from a common ancestor.

Incorrect. You've got the arrow of implication backwards. We do not assume that life is commonly descended. Instead, we conclude it. If life is cladistically arranged, then it necessarily follows that life descended from common ancestry. After all, there's no reason for unique creation to appear exactly like common descent.

Similarly with the genetic history: It necessarily follows that the shifting of genes implies common descent. If each one were uniquely created, there's no reason why the gene sequences would match up.

If A, then B. A, therefore B.

quote:
And expect me to believe you

No, I expect you to come up with a better response than, "I don't believe it." Part of the reason evolution is so strongly supported is because its predictions have borne out, because it solves so many problems, but it works so well.

quote:
At worst, you are begging the question. At best, you are affirming the consequent. Choose your fallacy.

How about neither.


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.
This message is a reply to:
 Message 39 by Doddy, posted 10-29-2007 8:51 AM Doddy has not yet responded

    
Rrhain
Member
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 45 of 49 (431240)
10-30-2007 4:00 AM
Reply to: Message 42 by Doddy
10-29-2007 8:04 PM


Doddy responds to crashfrog:

quote:
Because I'm going to draw a completely arbitrary line in the sand where you implicate that evolution between kinds can occur

And we have shown it to happen, over and over and over again. Here's an experiment you can do in the privacy of your own bio lab. It doesn't cost very much and the materials can be acquired from any decent biological supply house.

Take a single E. coli bacterium of K-type. This means the bacterium is susceptible to T4 phage. Let this bacterium reproduce until it forms a lawn. Then, infect the lawn with T4 phage.

What do we expect to happen? That's right, plaques should start to form and, eventually, the entire lawn will die. After all, every single bacterium in the lawn is descended from a single ancestor, so if the ancestor is susceptible, then all the offspring should be susceptible, too.

But what we actually see is that some colonies of bacteria in the lawn are not affected by the phage.

How can this be? Again, the entire lawn is descended from a single ancestor. They should all behave identically. If one is susceptible, then they're all susceptible. If one is immune, then they're all immune. This can't be an example of "adaptation" because if one could do it, they all could do it.

But since there is a discrepancy, we are left with only one conclusion: The bacteria evolved. There must be a genetic difference between the bacteria that are surviving and those that died.

Indeed, we call the new bacteria K-4 because they are immune to T4 phage.

But we're not done. Take a single K-4 bacterium and repeat the process: Let it reproduce to form a lawn and then infect the lawn with T4 phage.

What do we expect to happen? That's right: Absolutely nothing. All of the bacteria are descended from a single ancestor that is immune to T4 phage. Therefore, they all should survive and we shouldn't see any plaques form.

But we do. Plaques do, indeed start to form. How can this be? Again, all the bacteria in the lawn are descended from a single ancestor that was immune to T4 phage, so they shold all behave identically. If one is immune, then all are immune. There must be something else going on.

Something evolved, but the question is what. What evolved? Could it be the bacteria experiencing a reversion mutation back to K-type? No, that can't be it. Suppose any given bacteria did revert back to wild. It is surrounded by K-4 type who are immune to T4 phage. As soon as the lawn is infected, those few bacteria will die and immediately be replaced by the offspring of the immune K-4 bacteria. We would never see any plaques forming because the immune bacteria keep filling in any holes that appear.

So if it isn't the bacteria that evolved, it must be the phage. And, indeed, we call the new phage T4h as it has evolved a new host specificity.

There is a similar experiment where you take bacteria that have had their lactose operons removed and they evolve to be able to digest lactose again.

You might want to look up the information regarding the development of bacteria capable of digesting nylon oligimers. It's the result of a single frame-shift mutation.

Now, before you whine, "But it's still bacteria," let me say that of course it's still bacteria. A different KIND of bacteria. That's why we call it something different. This is an experiment that you can run in about a week. What sort of change were you expecting? An ostrich crawling out of the petri dish? That would completely destroy everything we thought we knew about how biology works.

We have plenty of other examples of evolutionary changes higher up the taxonomic tree, including the creation of new species, genera, even orders and families. Happening right in front of our eyes. Would you have us deny what we have directly witnessed?

quote:
therefore showing a relationship between humans and chimps.

Huh? Humans aren't descended from chimps and chimps aren't descended from humans.

I am not my cousin. My cousin is not me. I am not descended from my cousing. My cousin is not descended from me. Instead, we are descended from a common ancestor who is neither me nor my cousin: Our grandparents.

quote:
Or, because I'll adhere to the bronze age belief that the world is only 6000 years old, and that no amount of evolution could do such things.

But you've got the flood to deal with. Since it only happened about 4500 years ago, that would mean hyperevolution...changes happening at a rate so fast that no evolutionary biologist would agree and, because of the huge changes that would have to take place, would guarantee the extinction of all life on the planet as every single individual in the first generation would necessarily be a unique species, incapable of breeding with any other individual anywhere on the entire planet.

And thus, with no breeding pairs anywhere save the individuals from the ark, all life dies in the first generation after the flood.


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.
This message is a reply to:
 Message 42 by Doddy, posted 10-29-2007 8:04 PM Doddy has not yet responded

    
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