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Author Topic:   Micro v. Macro Creationist Challenge
Percy
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Posts: 16036
From: New Hampshire
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Member Rating: 3.0


Message 181 of 252 (816616)
08-08-2017 7:47 AM
Reply to: Message 180 by CRR
08-07-2017 9:28 PM


Re: Non homologous genes
CRR writes:

However if you go back to my past posts you will find that I disagree with equating macroevolution to speciation. I have said that speciation could be the result of either microevolution or macroevolution; where the critical difference is whether the mutation adds a significant amount of new genetic information.

Fruitful discussion requires agreement on definitions. As a starting point, here's the definition of macroevolution from Wikipedia:

quote:
Macroevolution is evolution on a scale at or above the level of species, in contrast with microevolution, which refers to smaller evolutionary changes of allele frequencies within a species or population.
Macroevolution and microevolution describe fundamentally identical processes on different time scales.

In your view, what's wrong with that definition?

--Percy


This message is a reply to:
 Message 180 by CRR, posted 08-07-2017 9:28 PM CRR has responded

Replies to this message:
 Message 183 by CRR, posted 08-09-2017 3:52 AM Percy has responded

    
Taq
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Member Rating: 3.1


Message 182 of 252 (816630)
08-08-2017 12:35 PM
Reply to: Message 180 by CRR
08-07-2017 9:28 PM


Re: Non homologous genes
CRR writes:

The explanation you seem to be advancing is that the non-homologous genes are explained by gene loss in both species.

The explanation is gene loss in the chimp lineage, but not in the human lineage.

This would mean that the common ancestor had all those non-homologous genes from both species.

As you referenced in previous posts, there are human and hominoid specific genes that were not expressed in the common ancestor of all apes.

What we see then is evolution by genetic loss. Then I guess it means that Microevolution is loss of genetic information in a population over time; and Macroevolution is when genetic loss results in morphological change and separation into new species, genera, etc.

So you think the differences between humans and other apes is due solely to gene loss? None of those differences are due to the emergence of new genes or alterations to existing genes?

However if you go back to my past posts you will find that I disagree with equating macroevolution to speciation. I have said that speciation could be the result of either microevolution or macroevolution; where the critical difference is whether the mutation adds a significant amount of new genetic information.

Do you consider the evolution of humans from a common ancestor shared with chimps to be macroevolution?

I think that's about 4% of PLCXD1. As I've said before I think I will put more weight on the Ensemble assessment of whether genes are homologous or not.

Ensembl is the one saying that there are orthologues of PLCXD1 in other primate genomes.


This message is a reply to:
 Message 180 by CRR, posted 08-07-2017 9:28 PM CRR has responded

Replies to this message:
 Message 184 by CRR, posted 08-09-2017 4:31 AM Taq has responded

  
CRR
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Posts: 578
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Message 183 of 252 (816660)
08-09-2017 3:52 AM
Reply to: Message 181 by Percy
08-08-2017 7:47 AM


Re: micro/macro definitions
There's a whole topic in that. The issue remains unresolved. I favour Durston's definitions myself.

[edit] Or from Message 107
microevolution = changes in gene frequencies and trait distributions that occur within populations and species
macroevolution = large evolutionary change, usually in morphology, typically refers to evolution of differences among populations that would warrant their plaecment in different genera or higher-level taxa

Edited by CRR, : [edit] Or from Message 107


This message is a reply to:
 Message 181 by Percy, posted 08-08-2017 7:47 AM Percy has responded

Replies to this message:
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CRR
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Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 184 of 252 (816661)
08-09-2017 4:31 AM
Reply to: Message 182 by Taq
08-08-2017 12:35 PM


Re: Non homologous genes
So for human genes that have no homologue in the chimp genome the explanation is gene loss in the chimp lineage, but not in the human lineage.

The Chimp genome has many genes that have, according to Ensemble, no homologue in the Human genome.
Is the explanation for this gene loss in the human lineage, but not in the chimp lineage?


This message is a reply to:
 Message 182 by Taq, posted 08-08-2017 12:35 PM Taq has responded

Replies to this message:
 Message 186 by Taq, posted 08-09-2017 10:41 AM CRR has responded

  
Percy
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Posts: 16036
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.0


Message 185 of 252 (816666)
08-09-2017 9:08 AM
Reply to: Message 183 by CRR
08-09-2017 3:52 AM


Re: micro/macro definitions
CRR writes:

The issue remains unresolved.

How can fruitful discussion about micro and macroevolution take place while disagreement about their definitions remains?

--Percy


This message is a reply to:
 Message 183 by CRR, posted 08-09-2017 3:52 AM CRR has not yet responded

    
Taq
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Posts: 7196
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Member Rating: 3.1


Message 186 of 252 (816677)
08-09-2017 10:41 AM
Reply to: Message 184 by CRR
08-09-2017 4:31 AM


Re: Non homologous genes
CRR writes:

So for human genes that have no homologue in the chimp genome the explanation is gene loss in the chimp lineage, but not in the human lineage.

As already shown, there are homologues on the X chromosome for the genes lost on the Y chromosome. The differences between the chimp and human Y chromosomes are due to loss in the chimp genome. For other genes, the mechanism for new genes is gene duplication in either lineage and/or evolution of new transcription factors upstream of regions that were not previously transcribed. It is all in the papers in you have been referencing.

The Chimp genome has many genes that have, according to Ensemble, no homologue in the Human genome.
Is the explanation for this gene loss in the human lineage, but not in the chimp lineage?

According to Ensembl there are parts of the human Y chromosome that are not present in the chimp Y chromosome, but are present in other ape Y chromosomes. Of the genes that are missing, there are homologues on the X chromosome. If Ensembl is what you trust, here is PLCXD1 mapped to the X chromosome at Ensembl:

http://www.ensembl.org/Homo_sapiens/Location/View?db=core...

Further down the X chromosome you can see SHOX, yet another of the genes on your list that has homologous sequence on the Y chromosome. See a pattern forming here? We can even see if there are homologues in the gorilla genome, and there are:

http://www.ensembl.org/Homo_sapiens/Location/Synteny?db=c...

Orangutan homologue? Yep, sure is:

http://www.ensembl.org/Homo_sapiens/Location/Synteny?g=EN...

This is not a human specific gene. The reason for the lack of a chimp homologue in the Y chromosome is gene loss as shown by the ape phylogeny.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 184 by CRR, posted 08-09-2017 4:31 AM CRR has responded

Replies to this message:
 Message 188 by CRR, posted 08-09-2017 6:41 PM Taq has responded

  
Taq
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Posts: 7196
Joined: 03-06-2009
Member Rating: 3.1


Message 187 of 252 (816678)
08-09-2017 10:42 AM
Reply to: Message 183 by CRR
08-09-2017 3:52 AM


Re: micro/macro definitions
CRR writes:

microevolution = changes in gene frequencies and trait distributions that occur within populations and species
macroevolution = large evolutionary change, usually in morphology, typically refers to evolution of differences among populations that would warrant their plaecment in different genera or higher-level taxa

All apes, including humans, are in separate genera. Would you agree that humans evolving from a common ancestor shared with chimps would be an example of macroevolution?


This message is a reply to:
 Message 183 by CRR, posted 08-09-2017 3:52 AM CRR has not yet responded

  
CRR
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From: Australia
Joined: 10-19-2016
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Message 188 of 252 (816711)
08-09-2017 6:41 PM
Reply to: Message 186 by Taq
08-09-2017 10:41 AM


Re: Non homologous genes between humans and chimps
Right now I'm focusing on non-homologous genes between humans and chimps. The Ensemble pages I linked previously show that humans have many genes that have no homologue anywhere in the chimp genome. You have already stated that the best explanation is gene loss in the chimp lineage, but not in the human lineage.

The Ensemble site also shows that chimps have many genes that have no homologue anywhere in the human genome. What do you think is the best explanation for this? Is it gene loss in the HUMAN lineage, but not in the CHIMP lineage?

We can look at orthologues later.


This message is a reply to:
 Message 186 by Taq, posted 08-09-2017 10:41 AM Taq has responded

Replies to this message:
 Message 189 by NoNukes, posted 08-09-2017 7:27 PM CRR has responded
 Message 191 by Taq, posted 08-10-2017 10:42 AM CRR has not yet responded

  
NoNukes
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Message 189 of 252 (816713)
08-09-2017 7:27 PM
Reply to: Message 188 by CRR
08-09-2017 6:41 PM


Re: Non homologous genes between humans and chimps
You have already stated that the best explanation is gene loss in the chimp lineage, but not in the human lineage.

Why wouldn't we expect something like a roughly equal amount of diversion between the species, assuming that they have a common ancestor?


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This message is a reply to:
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CRR
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Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 190 of 252 (816723)
08-10-2017 1:57 AM
Reply to: Message 189 by NoNukes
08-09-2017 7:27 PM


Re: Non homologous genes between humans and chimps
NoNukes writes:

Why wouldn't we expect something like a roughly equal amount of diversion between the species, assuming that they have a common ancestor?


I believe there are roughly equal numbers of non-homologous genes on each side.

The Ensemble pages I linked previously show that humans have many genes that have no homologue anywhere in the chimp genome. Taq has stated that the best explanation is gene loss in the chimp lineage, but not in the human lineage, since separation from the common ancestor. Do you agree with Taq?

The Ensemble site shows that chimps have many genes that have no homologue anywhere in the human genome.
What do you think is the best explanation for this?


This message is a reply to:
 Message 189 by NoNukes, posted 08-09-2017 7:27 PM NoNukes has acknowledged this reply

Replies to this message:
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Taq
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Posts: 7196
Joined: 03-06-2009
Member Rating: 3.1


Message 191 of 252 (816738)
08-10-2017 10:42 AM
Reply to: Message 188 by CRR
08-09-2017 6:41 PM


Re: Non homologous genes between humans and chimps
CRR writes:

Right now I'm focusing on non-homologous genes between humans and chimps.

I am focusing on the topic of the thread. That topic is a challenge given to ID/creationists to point to differences between the chimp and human genomes that could not be produced by known and observed mechanisms of mutagenesis. Gene loss is already a known and observed mechanism, so we can scratch that one off the list.

The Ensemble site also shows that chimps have many genes that have no homologue anywhere in the human genome.

No RNA homologue or no DNA homologue? You need to be specific, and list the genes you are talking about. If it is limited to just the end of the chimp Y-chromosome, then the explanation has already been given which is gene loss in the chimp genome as evidenced by the presence of those genes in other ape genomes.


This message is a reply to:
 Message 188 by CRR, posted 08-09-2017 6:41 PM CRR has not yet responded

  
Taq
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Posts: 7196
Joined: 03-06-2009
Member Rating: 3.1


Message 192 of 252 (816739)
08-10-2017 10:44 AM
Reply to: Message 190 by CRR
08-10-2017 1:57 AM


Re: Non homologous genes between humans and chimps
CRR writes:

The Ensemble pages I linked previously show that humans have many genes that have no homologue anywhere in the chimp genome. Taq has stated that the best explanation is gene loss in the chimp lineage, but not in the human lineage, since separation from the common ancestor. Do you agree with Taq?

I already showed you a reference dealing with those genes:

"The chimpanzee MSY contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor."
http://www.nature.com/...al/v463/n7280/full/nature08700.html

Are you saying that you disagree with this Nature paper?


This message is a reply to:
 Message 190 by CRR, posted 08-10-2017 1:57 AM CRR has responded

Replies to this message:
 Message 193 by CRR, posted 08-10-2017 7:50 PM Taq has responded

  
CRR
Member
Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 193 of 252 (816764)
08-10-2017 7:50 PM
Reply to: Message 192 by Taq
08-10-2017 10:44 AM


Re: Non homologous genes between humans and chimps
So then the human and chimp genomes both contain genes that have no homologue in the other.
The best evolutionary explanation for this is that the common ancestor species had all of those genes and each lineage has lost a large number of genes since separation.

Are you counting this gene loss as microevolution or macroevolution?


This message is a reply to:
 Message 192 by Taq, posted 08-10-2017 10:44 AM Taq has responded

Replies to this message:
 Message 194 by RAZD, posted 08-10-2017 8:26 PM CRR has responded
 Message 196 by Pressie, posted 08-11-2017 6:33 AM CRR has not yet responded
 Message 197 by Taq, posted 08-11-2017 10:55 AM CRR has not yet responded

  
RAZD
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Member Rating: 2.5


Message 194 of 252 (816767)
08-10-2017 8:26 PM
Reply to: Message 193 by CRR
08-10-2017 7:50 PM


Re: Non homologous genes between humans and chimps
The best evolutionary explanation for this is that the common ancestor species had all of those genes and each lineage has lost a large number of genes since separation.

No, the best evolutionary explanationis that since separation, some genes have been lost and some new genes have been gained.

You have not shown that evolution only results in loss, so you cannot base your hypothesis on incomplete information.

Enjoy.


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This message is a reply to:
 Message 193 by CRR, posted 08-10-2017 7:50 PM CRR has responded

Replies to this message:
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CRR
Member
Posts: 578
From: Australia
Joined: 10-19-2016
Member Rating: 1.1


Message 195 of 252 (816769)
08-11-2017 12:49 AM
Reply to: Message 194 by RAZD
08-10-2017 8:26 PM


Re: Non homologous genes between humans and chimps
RAZD writes:

No, the best evolutionary explanation is that since separation, some genes have been lost and some new genes have been gained.


That's interesting RAZD. Back at Message 182 regarding human genes that had no homologue in the chimp genome Taq said, "The explanation is gene loss in the chimp lineage, but not in the human lineage."
What then regarding chimp genes that have no homologue in the human genome?

Are there genes that have been gained since separation? A list would be good if you can find one.
Would gene gain be counted as micro or macroevolution?


This message is a reply to:
 Message 194 by RAZD, posted 08-10-2017 8:26 PM RAZD has acknowledged this reply

Replies to this message:
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