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Author Topic:   Micro v. Macro Creationist Challenge
Taq
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Posts: 8482
Joined: 03-06-2009


(1)
Message 177 of 252 (816361)
08-03-2017 10:57 AM
Reply to: Message 175 by CRR
08-02-2017 6:28 PM


Re: Human-chimp non homologues
CRR writes:

Strangely I put more weight on the papers published in Science and Nature than on your BLAT experiments.

That's strange since the Science and Nature papers are also saying that there is homologous and paralogous DNA in other primate species for human specific genes.

quote:
In this scenario, randomly occurring sequence combinations would form cryptic functional sites (for example, transcription initiation regions, splice sites and polyadenylation sites) and would come under a regulatory control to produce a distinct processed RNA transcript (Fig. 3). This RNA could initially function as an antisense or structural RNA39 and would eventually acquire a functional ORF from which a completely new protein could evolve. The most stringent criterion for indicating the involvement of this mechanism requires that the corresponding genomic region of the gene is present in outgroup organisms, but as a non-coding stretch that is neither transcribed nor translated.
http://www.nature.com/nrg/journal/v12/n10/full/nrg3053.html

That is from the paper that you referenced. It says exactly what I have been telling you. I would suggest reading the papers instead of projecting your wrongly held beliefs onto the papers.

Edited by Taq, : No reason given.


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 Message 175 by CRR, posted 08-02-2017 6:28 PM CRR has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 179 of 252 (816433)
08-04-2017 10:48 AM
Reply to: Message 178 by CRR
08-03-2017 8:15 PM


Re: Non homologous genes
CRR writes:

Let's go back a bit.
Are there non homologous genes when comparing humans to chimps?

I have no doubt that there could have been gene loss in either the chimp or human lineages. Do you think gene loss is an impediment to macroevolution? If not, then why mention it?

"The chimpanzee MSY [Y-chromosome] 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

A BLAT search also finds homologous DNA (first 1,000 bp) on the chimp X-chromosome for PLCXD1, the first gene on your Ensembl list below.

http://www.ensembl.org/Pan_troglodytes/Tools/Blast/Ticket

Ensemble website here shows many human genes as having no homologue anywhere in the chimp genome. (And many chimp genes that have no homologue in humans).

When you click on the orthologue button it finds homologous DNA in macaques, gorillas, and orangutans, to name a few. The orthologous DNA is found on the X-chromosome of those species. These genes are not human specific.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 178 by CRR, posted 08-03-2017 8:15 PM CRR has responded

Replies to this message:
 Message 180 by CRR, posted 08-07-2017 9:28 PM Taq has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


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

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


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
Member
Posts: 8482
Joined: 03-06-2009


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?


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 Message 183 by CRR, posted 08-09-2017 3:52 AM CRR has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


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
Member
Posts: 8482
Joined: 03-06-2009


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

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 197 of 252 (816786)
08-11-2017 10:55 AM
Reply to: Message 193 by CRR
08-10-2017 7:50 PM


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

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.

It depends on the gene. You need to be specific about which gene you are talking about.

Are you counting this gene loss as microevolution or macroevolution?

You tell us. Do you consider the evolution of humans and chimps from a common ancestor to be macroevolution or microevolution? Most creationists I know would count this as macroevolution, which is why I used it in this thread.


This message is a reply to:
 Message 193 by CRR, posted 08-10-2017 7:50 PM CRR has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


(1)
Message 198 of 252 (816787)
08-11-2017 11:00 AM
Reply to: Message 195 by CRR
08-11-2017 12:49 AM


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

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."

That is the explanation for the differences between the human y chromosome and the chimp y chromosome for the specific genes found at the end of the human y chromosome. I never said that it applies to every single difference between every chromosome.

Also, you are trying to conflate genes with DNA. Humans can have genes without homologues in the chimp genome, but they can still share the same DNA in those same regions. Gene is not a synonym for DNA. Genes are determined by RNA, not just DNA.

Are there genes that have been gained since separation? A list would be good if you can find one.

You already referenced the papers with those lists. Perhaps you should read your own references?

Would gene gain be counted as micro or macroevolution?

Do you think the evolution of humans from a common ancestor shared with chimps is microevolution?


This message is a reply to:
 Message 195 by CRR, posted 08-11-2017 12:49 AM CRR has responded

Replies to this message:
 Message 199 by CRR, posted 08-11-2017 5:29 PM Taq has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 200 of 252 (816827)
08-11-2017 6:10 PM
Reply to: Message 199 by CRR
08-11-2017 5:29 PM


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

No, because I don't think they evolved from a common ancestor.

If humans did evolve from a common ancestor shared with chimps, would you accept that as an example of macroevolution?


This message is a reply to:
 Message 199 by CRR, posted 08-11-2017 5:29 PM CRR has responded

Replies to this message:
 Message 202 by CRR, posted 08-13-2017 2:23 AM Taq has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 203 of 252 (816974)
08-14-2017 11:15 AM
Reply to: Message 202 by CRR
08-13-2017 2:23 AM


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

That would depend on what changes were required to produce the differences and how you define micro/macro evolution.

Can you point to a difference between the chimp and human genomes that could not be produced by known processes of mutagenesis? After all, this was the challenge given out in the opening post. It seems that we have come full circle, and you continue to avoid the question at hand.

As I've said before IF the common ancestor had all the human genes that chimps lack (and vice versa) and IF you define genetic loss as microevolution THEN it could be entirely microevolution.

You already cited a reference that new genes evolved in the human and chimp lineages. Did you forget that already?

This is why I originally said that you had arranged a "no win" challenge since you can make any assumptions you want and your definition of "microevolution" is so broad that such a scenario is permissible.

No, that is what you do. You are projecting.

I define macroevolution as the divergence of two lineages on separate evolutionary trajectories. This means that their genomes will diverge over time, and that is exactly what we have with chimps and humans.

Make the right assumptions about the common ancestor and allow enough deletions and you can explain anything!

Gene deletion is detected by the presence of the gene in the rest of the phylogeny. I already showed you that.

Of more interest would be to show that ALL genetic differences can be produced from a common ancestor having only genes that are orthologous within the great apes, and ensuring that all required changes produce no decrease in fitness and are fixed within the required time frame (allow 10 million years).

Turning the challenge around on your opponents without ever addressing the challenge is not a valid argument. The challenge in the opening post still stands.


This message is a reply to:
 Message 202 by CRR, posted 08-13-2017 2:23 AM CRR has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


(1)
Message 207 of 252 (817279)
08-16-2017 11:13 AM
Reply to: Message 205 by CRR
08-16-2017 7:34 AM


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

In message 1 Taq is trying to define microevolution as a single mutation event including almost any possible change, including an insertion of any size.

I am defining macroevolution as the differences between humans and chimps. Do you agree or disagree that the differences between humans and chimps constitutes macroevolution? Do you think humans and chimps are in the same created kind and share a common ancestor?

I am trying to find an example of macroevolution that we can both agree to so we don't quibble about definitions. If you want, we can use another primate genome that you think it better represents macroevolution if chimps and humans share a common ancestor in your version of creationism.

The de novo appearance of a fully functional orphan gene as a single insertion would therefore be counted as microevolution.

The whole point is that microevolutionary events accumulate to produce macroevolution, just as walking a mile is the accumulation of single steps.

There are no limits as to fitness, waiting time, or any other realistic constraint. Basically Taq allows himself a magic wand to accomplish any imaginable change in an arbitrary time.

You haven't shown that the differences between the human and chimp genomes violates any limits. Remember, the challenge is being given to you to show that microevolution can not produce the differences seen between the human and chimp genomes. Bare assertions aren't going to cut it.

Also, we can directly observe all of these types of mutations occurring in living species, so it is hardly magic. Magic is what you believe in. You think a supernatural deity magically poofed species into being. It seems that you are trying to accuse others of holding beliefs that you already hold. We call this "projection".

Edited by Taq, : No reason given.


This message is a reply to:
 Message 205 by CRR, posted 08-16-2017 7:34 AM CRR has responded

Replies to this message:
 Message 208 by CRR, posted 08-16-2017 6:37 PM Taq has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 210 of 252 (817398)
08-17-2017 11:06 AM
Reply to: Message 208 by CRR
08-16-2017 6:37 PM


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

Since it is only a hypothesis that humans and chimps developed from a common ancestor your definition is circular reasoning.

It is the same definition you are using. You said that macroevolution is the amount of change needed to produce a new "kind". Humans and chimps are in different kinds, according to your own posts.

I am defining macroevolution as a gain of a statistically significant amount of genetic information.

If the differences between the chimp and human genomes do not constitute "a gain of a statistically significant amount of genetic information" then you don't need a significant gain in order to produce macroevolution.

If the differences between the chimp and human genomes do constitute a significant gain, then those differences are the beneficial mutations that occurred through microevolution that accumulated to the point where they produced macroevolution.

Your choice.

Remind me, how do you explain that every human/chimp chromosome has genes that are non-homologous between humans and chimps?

A combination of gene loss, gene duplication, and evolution of transcription binding sites upstream of DNA that was previously not transcribed. Here is a review article if you want to read more:

quote:

Nat Rev Genet. 2011 Aug 31;12(10):692-702.

The evolutionary origin of orphan genes.

Tautz D1, Domazet-LoŇ°o T.

Abstract

Gene evolution has long been thought to be primarily driven by duplication and rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood. Orphan genes might arise from duplication and rearrangement processes followed by fast divergence; however, de novo evolution out of non-coding genomic regions is emerging as an important additional mechanism. This process appears to provide raw material continuously for the evolution of new gene functions, which can become relevant for lineage-specific adaptations.
https://www.ncbi.nlm.nih.gov/pubmed/21878963


Edited by Taq, : No reason given.


This message is a reply to:
 Message 208 by CRR, posted 08-16-2017 6:37 PM CRR has not yet responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 214 of 252 (818084)
08-23-2017 11:49 AM
Reply to: Message 211 by CRR
08-18-2017 6:12 PM


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

Microevolution: genetic variation that requires no statistically significant increase in functional information.

Macroevolution: genetic change that requires a statistically significant increase in functional information.

If the differences between the human and chimp genomes do not constitute a "statistically significant increase in functional information", then those definitions are meaningless since evolution would not need to produce this increase.

If the differences between the human and chimp genomes do constitute an increase, then you need to show how the known and natural processes of mutagenesis could not produce those differences.

Your choice.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 211 by CRR, posted 08-18-2017 6:12 PM CRR has responded

Replies to this message:
 Message 219 by CRR, posted 08-30-2017 12:11 AM Taq has responded

  
Taq
Member
Posts: 8482
Joined: 03-06-2009


(1)
Message 217 of 252 (818423)
08-28-2017 11:14 AM
Reply to: Message 215 by CRR
08-27-2017 3:48 AM


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

If humans have a gene that has no homologue in chimps but has homologues in Orangutan, Gorilla, and Macaque what is the best explanation?

Gene loss in the chimp lineage.

Similarly there are genes in the chimp that have no homologue in humans but does have homologues in Orangutan, Gorilla, and Macaque. How would you explain this?

Gene loss in the human lineage.

It seems that you find many genes that appear to be shared across several species but are missing from some. What does this indicate for how you view primate evolution?

If the gene loss/gains follow a phylogenetic pattern, it points to common ancestry. A common designer could remove and add genes in almost any pattern, but evolution can only produce one pattern, and that pattern is a phylogeny. For example, a common designer could add gene BBB to gorillas, humans, and macaques, but no other primate species. However, we don't see that pattern. We see that gene gains and losses follow a branching structure as we would expect from evolution and common ancestry.


This message is a reply to:
 Message 215 by CRR, posted 08-27-2017 3:48 AM CRR has not yet responded

  
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