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Topic: Functional roles of Aves class-specific cis-regulatory elements (Read 387 times) previous topic - next topic

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  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #50
I will be leaving this shortly.
worth repeating
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #51
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

The non-coding regulatory sequences produce the myriad differences (phenotypes) between different types of birds.
And
Quote
very few [protein coding] lineage-specific genes emerged in the avian genome
I suggest that if "very few [protein coding] lineage-specific genes emerged in the avian genome", then very few changes were required in the evolution from bird ancestor to bird.
The non-coding regulatory sequences the study found, produce the myriad differences (phenotypes) between different types of birds.
If very few changes were required in the evolution from bird ancestor to bird then the ancestor must have been quite similar to the first birds.
This is a problem for the dino to bird theory since dinosaurs are completely different than birds.
So we need to look for an ancestor that is similar to the first birds.
Pterosaurs are similar to the first birds. Pterosaur as ancestor is consistent with the evidence of the study. That explains the "surprising" evidence.

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #52
http://www.ucmp.berkeley.edu/diapsids/avians.html
Quote
The first birds shared the following major skeletal characteristics with many coelurosaurian dinosaurs (especially those of their own clade, the Maniraptora, which includes Velociraptor):

Pubis (one of the three bones making up the vertebrate pelvis) shifted from an anterior to a more posterior orientation (see Saurischia), and bearing a small distal "boot".
Elongated arms and forelimbs and clawed manus (hands).
Large orbits (eye openings in the skull).
Flexible wrist with a semi-lunate carpal (wrist bone).
Hollow, thin-walled bones.
3-fingered opposable grasping manus (hand), 4-toed pes (foot); but supported by 3 main toes.
Reduced, posteriorly stiffened tail.
Elongated metatarsals (bones of the feet between the ankle and toes).
S-shaped curved neck.
Erect, digitgrade (ankle held well off the ground) stance with feet postitioned directly below the body.
Similar eggshell microstructure.
Teeth with a constriction between the root and the crown.
Functional basis for wing power stroke present in arms and pectoral girdle (during motion, the arms were swung down and forward, then up and backwards, describing a "figure-eight" when viewed laterally).
Expanded pneumatic sinuses in the skull.
Five or more vertebrae incorporated into the sacrum (hip).
Straplike scapula (shoulder blade).
Clavicles (collarbone) fused to form a furcula (wishbone).
Hingelike ankle joint, with movement mostly restricted to the fore-aft plane.
Secondary bony palate (nostrils open posteriorly in throat).
Possibly feathers... this awaits more study. Small, possibly feathered dinosaurs were recently found in China. It appears that many coelurosaurs were cloaked in an external fibrous covering that could be called "protofeathers."
How many of those characteristics are shared by pterosaurs?

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #53
Faid quotes an early error I made in comparing early birds to Compsognathus. I made that error because a great deal of the literature asserted that point and I accepted it because of that, before I looked into it myself. When I analyzed it myself I found it was wrong and have repeatedly corrected that initial error. Not worth arguing about.

  • Faid
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #54
Quote
So we need to look for an ancestor that is similar to the first birds.
Quote from: Socrates;1684678
The body of Archaeopteryx is that of a Compsognathus.

So something like a Compsognathus is a safe bet.

IOW, a theropod dinosaur.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #55
http://www.ucmp.berkeley.edu/diapsids/avians.html
Quote
The first birds shared the following major skeletal characteristics with many coelurosaurian dinosaurs (especially those of their own clade, the Maniraptora, which includes Velociraptor):

Pubis (one of the three bones making up the vertebrate pelvis) shifted from an anterior to a more posterior orientation (see Saurischia), and bearing a small distal "boot".
Elongated arms and forelimbs and clawed manus (hands).
Large orbits (eye openings in the skull).
Flexible wrist with a semi-lunate carpal (wrist bone).
Hollow, thin-walled bones.
3-fingered opposable grasping manus (hand), 4-toed pes (foot); but supported by 3 main toes.
Reduced, posteriorly stiffened tail.
Elongated metatarsals (bones of the feet between the ankle and toes).
S-shaped curved neck.
Erect, digitgrade (ankle held well off the ground) stance with feet postitioned directly below the body.
Similar eggshell microstructure.
Teeth with a constriction between the root and the crown.
Functional basis for wing power stroke present in arms and pectoral girdle (during motion, the arms were swung down and forward, then up and backwards, describing a "figure-eight" when viewed laterally).
Expanded pneumatic sinuses in the skull.
Five or more vertebrae incorporated into the sacrum (hip).
Straplike scapula (shoulder blade).
Clavicles (collarbone) fused to form a furcula (wishbone).
Hingelike ankle joint, with movement mostly restricted to the fore-aft plane.
Secondary bony palate (nostrils open posteriorly in throat).
Possibly feathers... this awaits more study. Small, possibly feathered dinosaurs were recently found in China. It appears that many coelurosaurs were cloaked in an external fibrous covering that could be called "protofeathers."
How many of those characteristics are shared by pterosaurs?
Check the blog.

  • Faid
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #56
Faid quotes an early error I made in comparing early birds to Compsognathus. I made that error because a great deal of the literature asserted that point and I accepted it because of that, before I looked into it myself. When I analyzed it myself I found it was wrong and have repeatedly corrected that initial error. Not worth arguing about.
That is a lie.

You did not "look into anything" yourself. You pompously asserted that it was obvious the body of Archie was "that of a compsognathus", when you were trying to claim Archie was a "forgery". When you realized that didn't work, you changed your tune and started to claim it was different. But you NEVER justified your change in any 'analysis'- if you had, you would have been able to say why you were fooled before.


You're just pretending. And you know we all know it.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #57
http://www.ucmp.berkeley.edu/diapsids/avians.html
Quote
The first birds shared the following major skeletal characteristics with many coelurosaurian dinosaurs (especially those of their own clade, the Maniraptora, which includes Velociraptor):

Pubis (one of the three bones making up the vertebrate pelvis) shifted from an anterior to a more posterior orientation (see Saurischia), and bearing a small distal "boot".
Elongated arms and forelimbs and clawed manus (hands).
Large orbits (eye openings in the skull).
Flexible wrist with a semi-lunate carpal (wrist bone).
Hollow, thin-walled bones.
3-fingered opposable grasping manus (hand), 4-toed pes (foot); but supported by 3 main toes.
Reduced, posteriorly stiffened tail.
Elongated metatarsals (bones of the feet between the ankle and toes).
S-shaped curved neck.
Erect, digitgrade (ankle held well off the ground) stance with feet postitioned directly below the body.
Similar eggshell microstructure.
Teeth with a constriction between the root and the crown.
Functional basis for wing power stroke present in arms and pectoral girdle (during motion, the arms were swung down and forward, then up and backwards, describing a "figure-eight" when viewed laterally).
Expanded pneumatic sinuses in the skull.
Five or more vertebrae incorporated into the sacrum (hip).
Straplike scapula (shoulder blade).
Clavicles (collarbone) fused to form a furcula (wishbone).
Hingelike ankle joint, with movement mostly restricted to the fore-aft plane.
Secondary bony palate (nostrils open posteriorly in throat).
Possibly feathers... this awaits more study. Small, possibly feathered dinosaurs were recently found in China. It appears that many coelurosaurs were cloaked in an external fibrous covering that could be called "protofeathers."
How many of those characteristics are shared by pterosaurs?
Check the blog.
Let me repeat an important point concerning:
Quote
The first birds shared the following major skeletal characteristics with many coelurosaurian dinosaurs (especially those of their own clade, the Maniraptora, which includes Velociraptor)
The first birds shared skeletal characteristics with many Paravians. But Paravians are not dinosaurs.
I have made this point many, many times.

  • Faid
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #58
And you can make it twice as many. That won't make it any less wrong.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #59
http://www.ucmp.berkeley.edu/diapsids/avians.html
Quote
The first birds shared the following major skeletal characteristics with many coelurosaurian dinosaurs (especially those of their own clade, the Maniraptora, which includes Velociraptor):

Pubis (one of the three bones making up the vertebrate pelvis) shifted from an anterior to a more posterior orientation (see Saurischia), and bearing a small distal "boot".
Elongated arms and forelimbs and clawed manus (hands).
Large orbits (eye openings in the skull).
Flexible wrist with a semi-lunate carpal (wrist bone).
Hollow, thin-walled bones.
3-fingered opposable grasping manus (hand), 4-toed pes (foot); but supported by 3 main toes.
Reduced, posteriorly stiffened tail.
Elongated metatarsals (bones of the feet between the ankle and toes).
S-shaped curved neck.
Erect, digitgrade (ankle held well off the ground) stance with feet postitioned directly below the body.
Similar eggshell microstructure.
Teeth with a constriction between the root and the crown.
Functional basis for wing power stroke present in arms and pectoral girdle (during motion, the arms were swung down and forward, then up and backwards, describing a "figure-eight" when viewed laterally).
Expanded pneumatic sinuses in the skull.
Five or more vertebrae incorporated into the sacrum (hip).
Straplike scapula (shoulder blade).
Clavicles (collarbone) fused to form a furcula (wishbone).
Hingelike ankle joint, with movement mostly restricted to the fore-aft plane.
Secondary bony palate (nostrils open posteriorly in throat).
Possibly feathers... this awaits more study. Small, possibly feathered dinosaurs were recently found in China. It appears that many coelurosaurs were cloaked in an external fibrous covering that could be called "protofeathers."
How many of those characteristics are shared by pterosaurs?
Check the blog.
Let me repeat an important point concerning:
Quote
The first birds shared the following major skeletal characteristics with many coelurosaurian dinosaurs (especially those of their own clade, the Maniraptora, which includes Velociraptor)
The first birds shared skeletal characteristics with many Paravians. But Paravians are not dinosaurs.
I have made this point many, many times.
And nobody ever, anywhere, agreed with you. Why would anybody trust you on this?

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #60
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

The non-coding regulatory sequences produce the myriad differences (phenotypes) between different types of birds.
And
Quote
very few [protein coding] lineage-specific genes emerged in the avian genome
I suggest that if "very few [protein coding] lineage-specific genes emerged in the avian genome", then very few changes were required in the evolution from bird ancestor to bird.
The non-coding regulatory sequences the study found, produce the myriad differences (phenotypes) between different types of birds.
If very few changes were required in the evolution from bird ancestor to bird then the ancestor must have been quite similar to the first birds.
This is a problem for the dino to bird theory since dinosaurs are completely different than birds.
So we need to look for an ancestor that is similar to the first birds.
Pterosaurs are similar to the first birds. Pterosaur as ancestor is consistent with the evidence of the study. That explains the "surprising" evidence.
The evidence is only surprising if you assume that birds evolved from dinosaurs. The evidence is not surprising if you assume that birds evolved from pterosaurs.

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #61
< clip pointless self-quote >
< clip pointless self-quote >
< clip pointless self-quote >
< clip pointless self-quote >
< clip pointless self-quote >
< clip pointless self-quote >
< clip pointless self-quote >

The evidence is only surprising if you assume that birds evolved from dinosaurs. The evidence is not surprising if you assume that birds evolved from pterosaurs.
And what evidence is that, "Socrates" ?

You obviously haven't a clue.

Because the observations described by Seki et al. are no more or less "surprising", whether birds are descended from dinosaurs, pterosaurs, or salamanders.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #62
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

The non-coding regulatory sequences produce the myriad differences (phenotypes) between different types of birds.
And
Quote
very few [protein coding] lineage-specific genes emerged in the avian genome
I suggest that if "very few [protein coding] lineage-specific genes emerged in the avian genome", then very few changes were required in the evolution from bird ancestor to bird.
The non-coding regulatory sequences the study found, produce the myriad differences (phenotypes) between different types of birds.
If very few changes were required in the evolution from bird ancestor to bird then the ancestor must have been quite similar to the first birds.
This is a problem for the dino to bird theory since dinosaurs are completely different than birds.
So we need to look for an ancestor that is similar to the first birds.
Pterosaurs are similar to the first birds. Pterosaur as ancestor is consistent with the evidence of the study. That explains the "surprising" evidence.
The evidence is only surprising if you assume that birds evolved from dinosaurs. The evidence is not surprising if you assume that birds evolved from pterosaurs.
People will pretend not to get this. In fact the evidence from the study is exactly what the pterosaur to bird theory would predict. Not much point in discussing with folks who are pretending.
If anyone cares to go beyond pretending let me know. Otherwise I will leave it at that.

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #63
Speaking of pretending:
Someone earlier tried to pretend I misunderstood the study. It did not work then and it does not work now. I am not wasting time on that.
If this is usual, then why were they surprised? Face it, this is very unusual. But if someone knows better than these surprised scientists then give us your explanation.
Better yet, just admit you have no idea. 
If someone knows better than these surprised scientists then give us your explanation. Pretending I do not understand this subject does not cut it.

Explanation ... for WHAT?
WHAT do you think is "unusual"?
"Unusual" relative to WHAT?
needs repeating, apparently.
You really have no idea, have you?
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins