By: Seid Dzekovic
The family of NANOG pseudogenes gives us persuasive evidence that humans and chimpanzees shared a common ancestor.
Before we jump into it,we should posses at least some basic knowledge about pseudogenes and their types.
Pseudogenes are genes which are related to fully functional genes. They have lost at least some functionality, though they aren't necessarily nonfunctional. Creationists often falsely claim that non-functionality is inherent in the idea of pseudogenes. The function that they do have may be a modification of an ancestral gene.
They usually accumulate multiple mutations, and sometimes they can perform regulatory functions.
We'll concentrate on processed and non-processed pseudogenes since only these 2 types exsist in the family of NANOG pseudogenes.
I'll use the definitions from Wikipedia, since I've checked and their definitions and descriptions are accurate:
Processed or retrotransposed pseudogenes:
"In the process of retrotransposition, a portion of the mRNA or hnRNAtranscript of a gene is spontaneously reverse transcribed back into DNA and inserted into chromosomal DNA."
Non-processed pseudogenes:
"Non-processed (or duplicated) pseudogenes. Gene duplication is another common and important process in the evolution of genomes. A copy of a functional gene may arise as a result of a gene duplication event caused by homologous recombination at, for example, repetitive sine sequences on misaligned chromosomes and subsequently acquire mutations that cause the copy to lose the original gene's function. Duplicated pseudogenes usually have all the same characteristics as genes, including an intact exon-intron structure and regulatory sequences."
So now when we know how these pseudogenes come into existence,we are going to talk about them in more details.
Human genome consists of 11 NANOG pseudogenes,10 retropseudogenes and 1 duplication pseudogene.
When Daniel Fairbanks and Peter Maughan examined chimpanzee's genome, they found 10 of those at their expected orthologous chromosomal positions.
One of them (NANOGP8) was absent from chimpanzee's genome and we'll talk about that a bit later.
As noted above, 10 of those pseudogenes were found at the very same chromosomal position where we find them in human genome:
Functional NANOG pseudogene:
Chromosome 12 in both genomes;
NANOG P1: Chromosome 12 in both genomes;
NANOG P2: Chromosome 2 in human genome and 2B in chimpanzee's genome. *Human chromosome 2 consists of 2A and 2B chimp chromosomes, in other words what is a single chromosome in humans are two separated chromosomes in chimps because of chromosome fusion in humans;
The family of NANOG pseudogenes gives us persuasive evidence that humans and chimpanzees shared a common ancestor.
Before we jump into it,we should posses at least some basic knowledge about pseudogenes and their types.
Pseudogenes are genes which are related to fully functional genes. They have lost at least some functionality, though they aren't necessarily nonfunctional. Creationists often falsely claim that non-functionality is inherent in the idea of pseudogenes. The function that they do have may be a modification of an ancestral gene.
They usually accumulate multiple mutations, and sometimes they can perform regulatory functions.
We'll concentrate on processed and non-processed pseudogenes since only these 2 types exsist in the family of NANOG pseudogenes.
I'll use the definitions from Wikipedia, since I've checked and their definitions and descriptions are accurate:
Processed or retrotransposed pseudogenes:
"In the process of retrotransposition, a portion of the mRNA or hnRNAtranscript of a gene is spontaneously reverse transcribed back into DNA and inserted into chromosomal DNA."
Non-processed pseudogenes:
"Non-processed (or duplicated) pseudogenes. Gene duplication is another common and important process in the evolution of genomes. A copy of a functional gene may arise as a result of a gene duplication event caused by homologous recombination at, for example, repetitive sine sequences on misaligned chromosomes and subsequently acquire mutations that cause the copy to lose the original gene's function. Duplicated pseudogenes usually have all the same characteristics as genes, including an intact exon-intron structure and regulatory sequences."
So now when we know how these pseudogenes come into existence,we are going to talk about them in more details.
Human genome consists of 11 NANOG pseudogenes,10 retropseudogenes and 1 duplication pseudogene.
When Daniel Fairbanks and Peter Maughan examined chimpanzee's genome, they found 10 of those at their expected orthologous chromosomal positions.
One of them (NANOGP8) was absent from chimpanzee's genome and we'll talk about that a bit later.
As noted above, 10 of those pseudogenes were found at the very same chromosomal position where we find them in human genome:
Functional NANOG pseudogene:
Chromosome 12 in both genomes;
NANOG P1: Chromosome 12 in both genomes;
NANOG P2: Chromosome 2 in human genome and 2B in chimpanzee's genome. *Human chromosome 2 consists of 2A and 2B chimp chromosomes, in other words what is a single chromosome in humans are two separated chromosomes in chimps because of chromosome fusion in humans;
NANOG P3: Chromosome 6 in both genomes;
NANOG P4: Chromosome 7 in both genomes;
NANOG P5: Chromosome 9 in both genomes;
NANOG P6: Chromosome 10 in both genomes;
NANOG P7: Chromosome 14 in both genomes;
NANOG P8: Chromosome 15 in humans and absent in chimp genome;
NANOG P9: Chromosome X in both genomes;
NANOG P10: Chromosome X in both genomes;
NANOG P11: Chromosome 6 in both genomes;
Evolutionary implications of NANOG pseudogenes:
*These implications certainly aren't ad hoc since I am going to give justification for every one of my claims and I am going to show why are they consistent with evolutionary common descent. If you don't agree with my justifications or think that they are ad hoc, be sure to tell us exactly why and we'll be more than happy to discuss it.
So, since evolutionary theory teaches that humans and chimpanzees shared common ancestors at some point, we would expect them to share at least some of these copies since copies would originate in the common ancestor.
Copies which predated the divergence should exist in both lineages and if we find a pseudogene copy only in human or chimp genome, then that copy HAS to postdate the divergence.
We should also expect to see the same copying errors included since errors occurred in the common ancestor and should exsist in both genomes.
And all this is exactly what we found when examined NANOG pseudogenes in two respective lineages:
- There are 10 shared pseudogenes between humans and chimps;
- Two shared retropseudogenes lack the poly-(A) tails characteristic of most retropseudogenes, indicating that copying errors occurred during their creation.
- The NANOG pseudogene on the X chromosome has 21 (of 22) changes which are identical in the pseudogen of humans and chimpanzees;
Why does the NANOG P8 only exsist in human genome?
As noted above, pseudogene which is present in only one genome should postdate the divergence since otherwise there is no good reason for it to exist in one and to be absent from the other genome.
Relocations can be expected but the gene at least has to exist.
Fairbanks and Maughan conveniently solved the problem.
Namely, NANOG P8 has the same ALU element as functional NANOG gene in both genome
s.
Interestingly enough,all processed pseudogenes, NANOGP2, NANOGP3, NANOGP4,NA NOGP5, NANOGP6, NANOGP7, NANOGP9, NANOGP10 and NANOG11 lack this ALU element.
NANOG P4: Chromosome 7 in both genomes;
NANOG P5: Chromosome 9 in both genomes;
NANOG P6: Chromosome 10 in both genomes;
NANOG P7: Chromosome 14 in both genomes;
NANOG P8: Chromosome 15 in humans and absent in chimp genome;
NANOG P9: Chromosome X in both genomes;
NANOG P10: Chromosome X in both genomes;
NANOG P11: Chromosome 6 in both genomes;
Evolutionary implications of NANOG pseudogenes:
*These implications certainly aren't ad hoc since I am going to give justification for every one of my claims and I am going to show why are they consistent with evolutionary common descent. If you don't agree with my justifications or think that they are ad hoc, be sure to tell us exactly why and we'll be more than happy to discuss it.
So, since evolutionary theory teaches that humans and chimpanzees shared common ancestors at some point, we would expect them to share at least some of these copies since copies would originate in the common ancestor.
Copies which predated the divergence should exist in both lineages and if we find a pseudogene copy only in human or chimp genome, then that copy HAS to postdate the divergence.
We should also expect to see the same copying errors included since errors occurred in the common ancestor and should exsist in both genomes.
And all this is exactly what we found when examined NANOG pseudogenes in two respective lineages:
- There are 10 shared pseudogenes between humans and chimps;
- Two shared retropseudogenes lack the poly-(A) tails characteristic of most retropseudogenes, indicating that copying errors occurred during their creation.
- The NANOG pseudogene on the X chromosome has 21 (of 22) changes which are identical in the pseudogen of humans and chimpanzees;
Why does the NANOG P8 only exsist in human genome?
As noted above, pseudogene which is present in only one genome should postdate the divergence since otherwise there is no good reason for it to exist in one and to be absent from the other genome.
Relocations can be expected but the gene at least has to exist.
Fairbanks and Maughan conveniently solved the problem.
Namely, NANOG P8 has the same ALU element as functional NANOG gene in both genome
s.
Interestingly enough,all processed pseudogenes, NANOGP2, NANOGP3, NANOGP4,NA NOGP5, NANOGP6, NANOGP7, NANOGP9, NANOGP10 and NANOG11 lack this ALU element.
Thus, it is easy to conclude that this particular ALU insertion happened when all processed pseudogenes (from NANOGP2 to NANOGP11 without NANOGP8) already exsisted in a common ancestor of humans and chimps.
Since NANOGP8 copy has this ALU element, it is therefore easy to conclude that NANOGP8 indeed is the most recent pseudogene and that's why we see it in human genome exclusively.
However,to put it beyond any doubt, Fairbanks and Maughan calculated that based on assumption of mutation rate in humans, NANOGP8 is the most recent pseudogene and it originated around 5 mya,around the time of divergence.
Calculation isn't 100% accurate, since some genomes accumulate more mutations than the others, but anyways it is consistent with common descent, just where would we expect it to be if evolution were true.
It's worth mentioning that before I wrote this article, I was looking for creationist responses and not a single one of them had any refutation for evidence of common descent from NANOG family of pseudogenes.
The only thing I could find was from Casey Luskin's article on Discovery Institute's "Evolution news and views" where he argued that somehow NANOGP8 isn't a pseudogene since it is has function and it's critical member in Cancer stem cells.
His argument is both straw man and irony, since pseudogenes don't necessarily have to be nonfunctional and NANOGP8 is actually harmful, knocking the gene down could reduce the cancer malignancy, that's about it for being designed.
And he obviously didn't address NANOG as evidence of common descent since NANOGP8 is exclusive for humans and not chimpanzees as I've shown.
References:
Evolution of the NANOG pseudogene family in the human and chimpanzee genomes, Daniel J Fairbanks and Peter J Maughan https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457002/#!po=3.00000
GeneCards NANOGP8 https://www.genecards.org/cgi-bin/carddisp.pl?gene=NANOGP8&keywords=Nanogp4
Pseudogenes, types and origins
https://en.m.wikipedia.org/wiki/Pseudogene
Evolution totally unscientific totally fake
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