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Author Topic:   Discussion of Phylogenetic Methods
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 121 of 288 (795984)
12-20-2016 11:45 AM
Reply to: Message 35 by vaporwave
12-18-2016 1:26 PM


Re: Introduction
vaprowave writes:
Dogs and cats remain more similar to each other than either is to a jellyfish or a reptile. Surprise surprise...
Here is a mouse that, for one gene, is more similar to a jellyfish than any other vertebrate:
This mouse carries an exact copy of the jellyfish gene GFP (green fluorescent protein). How did it get there? These mice were DESIGNED by humans. We put the jellyfish gene in the mouse genome. If we can so easily violate a nested hierarchy, why couldn't God? Is God less powerful than humans?

This message is a reply to:
 Message 35 by vaporwave, posted 12-18-2016 1:26 PM vaporwave has replied

Replies to this message:
 Message 137 by vaporwave, posted 12-20-2016 6:08 PM Taq has replied

  
jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 122 of 288 (795985)
12-20-2016 11:50 AM
Reply to: Message 119 by Taq
12-20-2016 11:19 AM


More Fun With evidence
The big challenge for Creationists really comes down to evidence and explanation.
The reality is that humans look at whales and noticed they breathed air unlike fish that breathed water so we decided they were mammals.
The Creationist explanation for whales is God did it.
The reality is that humans look at whales' anatomy and noticed they seemed to show vestigial legs so we decided they were mammals that once lived on land.
The Creationist explanation for whales' anatomy is God did it.
The reality is that humans look at whales' anatomy and noticed they seemed to show vestigial legs so we decided they were mammals that once lived on land and so there should be some land animals that are closely related to whales.
The Creationist explanation for whales is God did it.
The reality is that humans look at whales' anatomy and noticed they seemed to show vestigial legs so we decided they were mammals that once lived on land and so there should be some land animals that are closely related to whales and once DNA analysis became possible found that whales and hippos were closely related.
The Creationist explanation for whales is God did it.
The reality is that humans look at whales' anatomy and noticed they seemed to show vestigial legs so we decided they were mammals that once lived on land and so there should be some land animals that are closely related to whales and once DNA analysis became possible found that whales and hippos were closely related and so there must have been a common ancestor to both whales and hippos.
The Creationist explanation for whales is God did it.
The fact and reality is that Creationism explains absolutely nothing and so has absolutely no value.

My Sister's Website: Rose Hill Studios My Website: My Website

This message is a reply to:
 Message 119 by Taq, posted 12-20-2016 11:19 AM Taq has replied

Replies to this message:
 Message 124 by Taq, posted 12-20-2016 12:15 PM jar has seen this message but not replied

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


Message 123 of 288 (795986)
12-20-2016 12:09 PM
Reply to: Message 26 by vaporwave
12-18-2016 12:12 PM


Re: Introduction
vaporwave writes:
Evolutionists fall back on a strange sort of metaphysics... they work off the assumption that if common descent were false, the pattern of morphology and DNA would necessarily be in discord. This assumption cannot be demonstrated or tested in any way of course.
That isn't the case.
The theory of evolution is the only theory which specifically predicts that we should see a strong correlation between phylogenies based on morphology and DNA. When a theory is able to predict these types of relationships between independent observations, then that is the theory we go with.
Creationism, on the other hand, makes no such prediction. It can't explain why we see a phylogenetic signal at all. It can't explain why wild type mice don't have exact copies of jellyfish genes. We already know that designers can mix and match genes as they see fit, because humans can do it. We know that other designs made by intelligent beings don't form statistically significant phylogenetic signals as we see with things such as cars, paintings, and buildings.
Creationism can not explain the most fundamental observations in biology, observations that go back to Linnaeus in the 18th century. Evolution can explain these observations perfectly.
The typical rebuttal here has the evolutionist quickly retreating to teleological territory and he begins rambling about how a Creator could do X or Y, etc....
We can simply point to the fact that no creationist can explain why we see a nested hierarchy instead of a different pattern of shared features.

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


(1)
Message 124 of 288 (795987)
12-20-2016 12:15 PM
Reply to: Message 122 by jar
12-20-2016 11:50 AM


Re: More Fun With evidence
jar writes:
The fact and reality is that Creationism explains absolutely nothing and so has absolutely no value.
Creationism has no value as a scientific theory, that much is true. Perhaps it has value as a dogmatic religious belief, but not as a scientific theory.
Creationists often accuse scientists of refusing to even consider creationism. The real problem is that Creationists haven't offered any scientific explanations to consider. They haven't offered testable predictions or mechanisms. They haven't produced testable and falsifiable explanations for the data we do have. They can't even explain the nested hierarchy that Linnaeus discovered in the 1700's.

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


Message 125 of 288 (795988)
12-20-2016 12:31 PM
Reply to: Message 101 by vaporwave
12-20-2016 8:31 AM


Re: The purpose of science
vaporwave writes:
I think even if molecular researchers had no concept of common ancestry they could have made similar predictions based off the simple idea that beings of similar anatomical properties are going to be more similar to each other in additional ways than not.
Google Chrome on the PC and Mac look almost exactly the same from the outside, yet the machine code underneath is entirely different.
Why wouldn't we think the same of different species? Why couldn't we see very different DNA even if their morphology is similar?
And why do we see areas of genomes that are more similar than others if creationism is true? Why should we see more similarities in exons than in introns when we compare the cat and dog genomes? How does creationism explain that?

This message is a reply to:
 Message 101 by vaporwave, posted 12-20-2016 8:31 AM vaporwave has replied

Replies to this message:
 Message 128 by vaporwave, posted 12-20-2016 2:56 PM Taq has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 126 of 288 (795989)
12-20-2016 2:37 PM
Reply to: Message 116 by Taq
12-20-2016 10:49 AM


Re: The purpose of phylogenetics
When you organize 30 different taxa by morphology and by cytochrome c you get a perfect match between them:
Do you get a perfect match with cytochrome b ?
There is absolutely no reason that a creator would be forced to match cytochrome c sequences to morphology.
Okay, what's your point? There's no reason evolution would be forced to give rise to eukaryotes.

This message is a reply to:
 Message 116 by Taq, posted 12-20-2016 10:49 AM Taq has replied

Replies to this message:
 Message 127 by Taq, posted 12-20-2016 2:48 PM vaporwave has replied

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


Message 127 of 288 (795990)
12-20-2016 2:48 PM
Reply to: Message 126 by vaporwave
12-20-2016 2:37 PM


Re: The purpose of phylogenetics
vaporwave writes:
Do you get a perfect match with cytochrome b ?
Do you even care?
Okay, what's your point? There's no reason evolution would be forced to give rise to eukaryotes.
My point is that creationism can't explain the observations. Evolution can.

This message is a reply to:
 Message 126 by vaporwave, posted 12-20-2016 2:37 PM vaporwave has replied

Replies to this message:
 Message 129 by vaporwave, posted 12-20-2016 2:58 PM Taq has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 128 of 288 (795991)
12-20-2016 2:56 PM
Reply to: Message 125 by Taq
12-20-2016 12:31 PM


Re: The purpose of science
Google Chrome on the PC and Mac look almost exactly the same from the outside, yet the machine code underneath is entirely different.
Was the code for each version written by different people?
Why wouldn't we think the same of different species? Why couldn't we see very different DNA even if their morphology is similar?
Why expect this? If a particular template works, why change it?

This message is a reply to:
 Message 125 by Taq, posted 12-20-2016 12:31 PM Taq has replied

Replies to this message:
 Message 130 by Taq, posted 12-20-2016 3:02 PM vaporwave has replied
 Message 135 by RAZD, posted 12-20-2016 5:17 PM vaporwave has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 129 of 288 (795992)
12-20-2016 2:58 PM
Reply to: Message 127 by Taq
12-20-2016 2:48 PM


Re: The purpose of phylogenetics
Do you even care?
I just wonder why evolutionists always bring up cytochrome C but never cytochrome B. Is there a reason for that?

This message is a reply to:
 Message 127 by Taq, posted 12-20-2016 2:48 PM Taq has replied

Replies to this message:
 Message 131 by Dr Adequate, posted 12-20-2016 3:06 PM vaporwave has not replied
 Message 132 by Taq, posted 12-20-2016 3:14 PM vaporwave has replied

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


Message 130 of 288 (795993)
12-20-2016 3:02 PM
Reply to: Message 128 by vaporwave
12-20-2016 2:56 PM


Re: The purpose of science
vaporwave writes:
Was the code for each version written by different people?
The same person would have to write completely different codes due to the difference in operating systems and hardware.
The whole point is that there are nearly infinite methods for writing computer code to produce an identical looking web browser. The same applies to biological organisms. There are nearly infinite options for making a human with DNA, protein, and RNA. Changing the codon table is just one idea. You could change almost every third base in exons and still get the same protein. You could probably find pigments other than melanin to darken skin and hair. I could go on for days listing how a specific morphology does not require a specific DNA sequence.
vaporwave writes:
Why expect this? If a particular template works, why change it?
There are millions and billions of other templates that would work, so why reuse the same one?

This message is a reply to:
 Message 128 by vaporwave, posted 12-20-2016 2:56 PM vaporwave has replied

Replies to this message:
 Message 142 by vaporwave, posted 12-20-2016 6:41 PM Taq has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 131 of 288 (795994)
12-20-2016 3:06 PM
Reply to: Message 129 by vaporwave
12-20-2016 2:58 PM


Re: The purpose of phylogenetics
I just wonder why evolutionists always bring up cytochrome C but never cytochrome B. Is there a reason for that?
A Google Scholar search for "cytochrome b" phylogeny gets 36,200 hits. So the reason for the thing you made up in your head is very much a question that we should be asking you and not vice versa.

This message is a reply to:
 Message 129 by vaporwave, posted 12-20-2016 2:58 PM vaporwave has not replied

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


(1)
Message 132 of 288 (795995)
12-20-2016 3:14 PM
Reply to: Message 129 by vaporwave
12-20-2016 2:58 PM


Re: The purpose of phylogenetics
I just wonder why evolutionists always bring up cytochrome C but never cytochrome B. Is there a reason for that?
Probably for the reason that cytochrome c is somatic while cytochrome b is mitochondrial. This is from Wikipedia:
"Cytochrome c is a highly conserved protein across the spectrum of species, found in plants, animals, and many unicellular organisms. This, along with its small size (molecular weight about 12,000 daltons),[6] makes it useful in studies of cladistics.[7]"
Added in edit . . .
This is also from Wikipedia:
"Cytochrome b is commonly used as a region of mitochondrial DNA for determining phylogenetic relationships between organisms, due to its sequence variability. It is considered to be most useful in determining relationships within families and genera. "
Variation in cytB is higher than cytC, making cytC the choice for comparing more distantly related organisms.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 129 by vaporwave, posted 12-20-2016 2:58 PM vaporwave has replied

Replies to this message:
 Message 136 by vaporwave, posted 12-20-2016 6:04 PM Taq has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 133 of 288 (795996)
12-20-2016 4:39 PM
Reply to: Message 119 by Taq
12-20-2016 11:19 AM


Re: More Fun With Cytochrome C
In this phylogeny we can see that A and B share a recent common ancestor. A and B also share the SAME common ancestor with C. When you trace the phylogeny to where B and C meet it is the same node where A and C meet. Therefore, the genetic (i.e. evolutionary) distance between A and C is the same as that for B and C. A and B are genetically equidistant from C. We should see this equidistance in genetic data if evolution is true.
In other words, we can test the genetic phylogenies to see whether they match this prediction or no.
Humans and mice are the A and B in our model. Chickens are the C. Therefore, we should see similar genetic distance between humans and chickens as we see for mice and chickens. So do we? We sure do:
And we should see the same genetic distance from chimp to rhesus monkey as from human to rhesus monkey?

we are limited in our ability to understand
by our ability to understand
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This message is a reply to:
 Message 119 by Taq, posted 12-20-2016 11:19 AM Taq has replied

Replies to this message:
 Message 134 by Taq, posted 12-20-2016 5:02 PM RAZD has seen this message but not replied

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


(2)
Message 134 of 288 (795999)
12-20-2016 5:02 PM
Reply to: Message 133 by RAZD
12-20-2016 4:39 PM


Re: More Fun With Cytochrome C
RAZD writes:
And we should see the same genetic distance from chimp to rhesus monkey as from human to rhesus monkey?
Yes, although the differences aren't as dramatic.
You can do the same for any other species trio at Homologene:
HomoloGene - NCBI
(I don't know if this link works for anyone, let me know if you get sent to a weird page)
It has all of the possible comparisons between their model organisms if you scroll down. We could look at human, chicken, and fruit fly.
human v. chicken = 81.6%
human v. fruit fly = 71.9%
chicken v. fruit fly = 71.6%
As expected, we see the same difference between human and fruit fly as we do between chicken and fruit fly since both chickens and humans share the same common ancestor with fruit flies (as do all vertebrates). Other fun trios on that list are cows:frogs:round worms and dogs:rats:yeast.

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 135 of 288 (796001)
12-20-2016 5:17 PM
Reply to: Message 128 by vaporwave
12-20-2016 2:56 PM


pro template and con template
Why wouldn't we think the same of different species? Why couldn't we see very different DNA even if their morphology is similar?
Why expect this? If a particular template works, why change it?
Let me introduce you to a couple of little cuties for the purpose of this discussion:
The Great Creationist Fossil Failure, Message 1121: Curiously, I have argued that the concept of clades is the closest parallel in evolutionary terminology to the creationist concept of kinds -- each reproduce after their own kind. A member of the wolf clade will always be a member of the wolf clade and not become a member of another clade via evolution. This is generally viewed by creationists as "micro" evolution.
quote:
Analogy: Squirrels and Sugar Gliders
Beyond being cute and cuddly, flying squirrels and sugar gliders have many striking similarities: big eyes, a white belly, and a thin piece of skin stretched between their arms and legs, a trait which helps them "glide" and remain stable when leaping from high places.
But sugar gliders and flying squirrels also have some key differences. Most importantly, they reproduce and bear their babies in fundamentally different ways:
Flying squirrels and sugar gliders are only distantly related. So why do they look so similar then? Their gliding "wings" and big eyes are analogous structures. Natural selection independently adapted both lineages for similar lifestyles: leaping from treetops (hence, the gliding "wings") and foraging at night (hence, the big eyes).

So while Diportodontia is a different clade from Rodentia, and it is a member of the marsupial mammal clade and not the placental mammal clade they both are members of the mammal clade ... there IS a common ancestor population they evolved from, (and we can go back further) ... BUT while each have not evolved "out of their (Diportodontia, Rodentia) clades" they have arrived at a similar point through selection and mutations.
Message 1140 in the same thread details the phylogeny from common ancestor to Metatheria to Diprotodontia to Petauridae ...
The sugar glider (Petaurus breviceps) is a small, omnivorous, arboreal, and nocturnal gliding possum belonging to the marsupial infraclass. ...
And it details the phylogeny from the common ancestor to Eutheria to Sciuridae to Pteromyini ...
Flying squirrels (scientifically known as Pteromyini or Petauristini) are a tribe of 44 species of squirrels in the family Sciuridae. ...
Did the squirrel become a possum or did the possum become a squirrel?
Message 101 (this thread): I think even if molecular researchers had no concept of common ancestry they could have made similar predictions based off the simple idea that beings of similar anatomical properties are going to be more similar to each other in additional ways than not.
Here we have very similar outward appearances but a phylogeny that says their common ancestor was very distant. Sugar gliders have more in common with kangaroos than Flying Squirrels, and Flying Squirrels have more in common with giraffes than Sugar Gliders.
Why expect this? If a particular template works, why change it?
Let's see if this answers your question:
The Great Creationist Fossil Failure, Message 1143: Convergent evolution disproves two common creationist concepts:
  1. that there is a limit to what microevolution can accomplish (dogs will always be dogs and not some other critter),
    Because starting from two entirely different lineages very similar species are developed via mutation and selection,
    and
  2. special creation, that each new species is created fully formed rather than descendant from other nearby species,
    When confronted with closely related species and shown the degree of similarity, the creationist claim is that god/s reused a template they had already developed.
    This argument is contradicted by and invalidated by convergent evolution, where these "templates" were NOT used, ... with no explanation for this failure.
When we look deeper we see that the differences outweigh the similarities, and that those differences are linked by homologies to ancestor populations that were more different between the two lineages until you get back to their common ancestor population, as demonstrated in Message 1140 in detail.
So the same "template" was not used for two very similar critters, but it was used for species that are not as similar appearing ...
... while evolution explains both cases with no difficulty.
Enjoy

we are limited in our ability to understand
by our ability to understand
RebelAmerican☆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)

This message is a reply to:
 Message 128 by vaporwave, posted 12-20-2016 2:56 PM vaporwave has replied

Replies to this message:
 Message 138 by vaporwave, posted 12-20-2016 6:20 PM RAZD has replied

  
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