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Jaws Vs Common Descent: Another Scientific Case Against Common Descent


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#1 Musibrique

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Posted 07 June 2016 - 01:16 AM

Jaws vs Common Descent: Another Failure For Common Descent:

According to common descent/evolutionists, humans are more closely related to bony fishes as they were evolutionary precursors before the evolution of tetrapods. Given that tetrapods are made up of bones and evolved from a common fish ancestor that was made up of bones and possibly lobe-fin like, it is more likely that tetrapods shared more closely related ancestry with that of ancestral bony fishes (Sarcopterygii/Actinopterygii) than boneless fishes that only have a skeleton made up of cartilage rather than true bones. Thus, under common descent, we would expect to find more similarites in ray-fin & lobe-fin aquatic group species since they have features of what evolutionists call true bones. On the other hand, chondrichthyes (sharks, elephant sharks, etc.) should have less similarities to humans according to common descent since they lack bone homology and also that we are more closely related to bony fishes like Sarcopterygii (lobe-fin fishes) & Actinopterygii (ray-fin fishes).

Yet, truth is stranger than fiction. A genome analysis of elephant sharks, a chimera cartilaginous shark (picture below), revealed that they share a large portion of their genes to humans and other mammals much more than the close relatives of tetrapods, bony fishes like zebrafishes.

The paper is entitled, "Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome"

Link: http://journals.plos...al.pbio.0050101

Here researchers compared the genome of a chimera elephant shark and compared it to that of human DNA. To their surprise, they found that humans actually share strong genetic similarity to boneless elephant sharks much more significantly than their close relatives, the bony fishes like zebrafish. As quoted in the paper:

"Of the 60,705 genic regions, 48,400 (80%) had significant similarity (cutoff at 1 × 10−10) to 11,805 human proteins. For the remaining genic regions, the assignment of putative orthology was based on significant matches to known proteins in cartilaginous fishes, chicken, fugu, zebrafish, and C. intestinalis. In total, the genic regions of the elephant shark assembly contain partial or complete sequences for 14,828 genes. This collection defines a minimal set of elephant shark genes that share strong sequence similarity with known vertebrate genes."

Here, researchers used a DNA library of 14,828 elephant shark genes and compared it to human DNA library which they used a total of 11,805 human genes. Elephant sharks contain only about a total of 17,449 protein coding genes, but researchers only used 84% of those genes (i.e. 14,828) for comparison. Out of the 14,828 shark genes they used, they found an 80% match to that of humans. When they compared the number of match genes to humans with that of bony fishes, they discovered that the similarity was less than that of boneless fishes.

Bony fishes missing genes in humans and other mammals?

Despite the fact that humans share strong genetic similarity with sharks, typically the chimera elephant shark, it was also found that those conserved genes were missing in bony/teleost fishes as well as in invertebrates. As quoted from the paper:

"A significant number of human genes that have orthologs in the elephant shark but not in teleost fishes are associated with male germ cells and fertilization (Table 1). These include genes that encode zona pellucida (ZP)–binding protein (Sp38) and ZP–sperm-binding protein (ZP-1). These are respectively expressed in the acrosome of sperm [34] and the ZP of oocytes [35] where they mediate the binding of sperm to ZP."

And

"Our analysis (see Materials and Methods) identified 154 human genes that have orthologs in mouse, dog, and the elephant shark, but not in the teleost fish genomes (Table S4). Out of the 154 genes, 85 (highlighted in Table S4) have no homologs in C. intestinalis, fruit fly, or the nematode worm. These are likely to be vertebrate-specific genes that have been lost in the teleost lineage."

Lost in the teleost lineage. In other words, these genes have disappeared in ray-fin/lobe-fin/teleost fishes but appeared earlier in chondrichthyes, which appeared first in the fossil record before the teleost lineage began (i.e. bony fishes) and also in tetrapod vertebrates, which appeared after the teleost lineage. Basically, these missing genes have appeared earlier, disappeared in between, and reappeared again later when tetrapod vertebrates were around even though those genes were even absent in invertebrates.

Sounds strange doesn't it?

"For 7,916 pairs, both genes have defined chromosomal coordinates. Interestingly, only 848 of these gene pairs (11%) are separated by <1 Mb in the zebrafish genome (median separation, 22 kb), and these are consolidated into 657 clusters, containing 1,489 genes in clusters of two to six genes per cluster (http://esharkgenome.imcb.a-star.edu.sg). When normalized to the number of unique gene pairs with defined chromosomal coordinates, the level of detectable conserved synteny for human is more than double that seen for zebrafish."

Wait, humans have more synteny (chromosome/gene blocks homology similarity) with sharks than their close bony fish relatives like zebrafishes? How can this be if humans/tetrapods presumably were related to bony fishes much more compared to the boneless aquatic creatures? Indeed, such similarity is hard to explain by common descent since it is hard to see how boneless sharks can share more genes with humans than that of bony fishes.

The only explanation these scientists have for why humans bizarrely share strong genes with sharks is by them presuming that those genes were lost in the bony fish lineage but then eventually reappeared before and again after when boneless fishes and tetrapod vertebrates were around. Of course, since common descent must be true, it must be that this was the case. Rather than relying on the evidence, these scientists sway away with speculative/wishful thinking ad hoc explanations to save the logic of common descent. Even though they observed a similarity that should not exist, they still hold on in defending common descent as if it was never falsified or at least conflicted.

Interestingly though, there are more similarities between humans and shark than just mere genes, they also seem to share very long strands of non-coding DNA sequences:

"Bejerano et al. [39] have identified 481 ultraconserved elements (UCEs) that are longer than 200 bp and perfectly conserved among the human, mouse, and rat genomes. These UCEs overlap transcribed and nontranscribed regions of the genome."

"Our analysis of the noncoding sequences in the elephant shark has shown that the elephant shark and human genomes contain twice as many conserved noncoding elements as that between human and zebrafish or fugu [40]. Taken together, these results suggest that a higher proportion of human sequences might be conserved in the elephant shark genome than in the teleost fish genomes."

Wow! So not only do humans and elephant sharks share similar coding genes, but they also share a very large portion of non-coding DNA that are more than 200 base pairs long and twice of that than found in bony fishes! Just how exactly did all those coding and non-coding regions get there in the human and chimera shark geneome when they don't share a common divergence together?

Hmm, it could be that instead of trying to explain this by common descent, there was a common designer, where this common designer used the same genetic blueprint, but modified it slightly in between of mammals and their unrelated cartilaginous fishes like the elephant shark. How can humans and other mammals share similar genes to something even more unrelated like a chimera shark, which presumably evolved 400 million years ago or so?

Another classical case of failure for common descent.
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#2 Blitzking

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Posted 08 June 2016 - 07:18 PM

Jaws vs Common Descent: Another Failure For Common Descent:

According to common descent/evolutionists, humans are more closely related to bony fishes as they were evolutionary precursors before the evolution of tetrapods. Given that tetrapods are made up of bones and evolved from a common fish ancestor that was made up of bones and possibly lobe-fin like, it is more likely that tetrapods shared more closely related ancestry with that of ancestral bony fishes (Sarcopterygii/Actinopterygii) than boneless fishes that only have a skeleton made up of cartilage rather than true bones. Thus, under common descent, we would expect to find more similarites in ray-fin & lobe-fin aquatic group species since they have features of what evolutionists call true bones. On the other hand, chondrichthyes (sharks, elephant sharks, etc.) should have less similarities to humans according to common descent since they lack bone homology and also that we are more closely related to bony fishes like Sarcopterygii (lobe-fin fishes) & Actinopterygii (ray-fin fishes).

Yet, truth is stranger than fiction. A genome analysis of elephant sharks, a chimera cartilaginous shark (picture below), revealed that they share a large portion of their genes to humans and other mammals much more than the close relatives of tetrapods, bony fishes like zebrafishes.

The paper is entitled, "Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome"

Link: http://journals.plos...al.pbio.0050101

Here researchers compared the genome of a chimera elephant shark and compared it to that of human DNA. To their surprise, they found that humans actually share strong genetic similarity to boneless elephant sharks much more significantly than their close relatives, the bony fishes like zebrafish. As quoted in the paper:

"Of the 60,705 genic regions, 48,400 (80%) had significant similarity (cutoff at 1 × 10−10) to 11,805 human proteins. For the remaining genic regions, the assignment of putative orthology was based on significant matches to known proteins in cartilaginous fishes, chicken, fugu, zebrafish, and C. intestinalis. In total, the genic regions of the elephant shark assembly contain partial or complete sequences for 14,828 genes. This collection defines a minimal set of elephant shark genes that share strong sequence similarity with known vertebrate genes."

Here, researchers used a DNA library of 14,828 elephant shark genes and compared it to human DNA library which they used a total of 11,805 human genes. Elephant sharks contain only about a total of 17,449 protein coding genes, but researchers only used 84% of those genes (i.e. 14,828) for comparison. Out of the 14,828 shark genes they used, they found an 80% match to that of humans. When they compared the number of match genes to humans with that of bony fishes, they discovered that the similarity was less than that of boneless fishes.

Bony fishes missing genes in humans and other mammals?

Despite the fact that humans share strong genetic similarity with sharks, typically the chimera elephant shark, it was also found that those conserved genes were missing in bony/teleost fishes as well as in invertebrates. As quoted from the paper:

"A significant number of human genes that have orthologs in the elephant shark but not in teleost fishes are associated with male germ cells and fertilization (Table 1). These include genes that encode zona pellucida (ZP)–binding protein (Sp38) and ZP–sperm-binding protein (ZP-1). These are respectively expressed in the acrosome of sperm [34] and the ZP of oocytes [35] where they mediate the binding of sperm to ZP."

And

"Our analysis (see Materials and Methods) identified 154 human genes that have orthologs in mouse, dog, and the elephant shark, but not in the teleost fish genomes (Table S4). Out of the 154 genes, 85 (highlighted in Table S4) have no homologs in C. intestinalis, fruit fly, or the nematode worm. These are likely to be vertebrate-specific genes that have been lost in the teleost lineage."

Lost in the teleost lineage. In other words, these genes have disappeared in ray-fin/lobe-fin/teleost fishes but appeared earlier in chondrichthyes, which appeared first in the fossil record before the teleost lineage began (i.e. bony fishes) and also in tetrapod vertebrates, which appeared after the teleost lineage. Basically, these missing genes have appeared earlier, disappeared in between, and reappeared again later when tetrapod vertebrates were around even though those genes were even absent in invertebrates.

Sounds strange doesn't it?

"For 7,916 pairs, both genes have defined chromosomal coordinates. Interestingly, only 848 of these gene pairs (11%) are separated by <1 Mb in the zebrafish genome (median separation, 22 kb), and these are consolidated into 657 clusters, containing 1,489 genes in clusters of two to six genes per cluster (http://esharkgenome.imcb.a-star.edu.sg). When normalized to the number of unique gene pairs with defined chromosomal coordinates, the level of detectable conserved synteny for human is more than double that seen for zebrafish."

Wait, humans have more synteny (chromosome/gene blocks homology similarity) with sharks than their close bony fish relatives like zebrafishes? How can this be if humans/tetrapods presumably were related to bony fishes much more compared to the boneless aquatic creatures? Indeed, such similarity is hard to explain by common descent since it is hard to see how boneless sharks can share more genes with humans than that of bony fishes.

The only explanation these scientists have for why humans bizarrely share strong genes with sharks is by them presuming that those genes were lost in the bony fish lineage but then eventually reappeared before and again after when boneless fishes and tetrapod vertebrates were around. Of course, since common descent must be true, it must be that this was the case. Rather than relying on the evidence, these scientists sway away with speculative/wishful thinking ad hoc explanations to save the logic of common descent. Even though they observed a similarity that should not exist, they still hold on in defending common descent as if it was never falsified or at least conflicted.

Interestingly though, there are more similarities between humans and shark than just mere genes, they also seem to share very long strands of non-coding DNA sequences:

"Bejerano et al. [39] have identified 481 ultraconserved elements (UCEs) that are longer than 200 bp and perfectly conserved among the human, mouse, and rat genomes. These UCEs overlap transcribed and nontranscribed regions of the genome."

"Our analysis of the noncoding sequences in the elephant shark has shown that the elephant shark and human genomes contain twice as many conserved noncoding elements as that between human and zebrafish or fugu [40]. Taken together, these results suggest that a higher proportion of human sequences might be conserved in the elephant shark genome than in the teleost fish genomes."

Wow! So not only do humans and elephant sharks share similar coding genes, but they also share a very large portion of non-coding DNA that are more than 200 base pairs long and twice of that than found in bony fishes! Just how exactly did all those coding and non-coding regions get there in the human and chimera shark geneome when they don't share a common divergence together?

Hmm, it could be that instead of trying to explain this by common descent, there was a common designer, where this common designer used the same genetic blueprint, but modified it slightly in between of mammals and their unrelated cartilaginous fishes like the elephant shark. How can humans and other mammals share similar genes to something even more unrelated like a chimera shark, which presumably evolved 400 million years ago or so?

Another classical case of failure for common descent.

 

 "Given that tetrapods are made up of bones and evolved from a common fish ancestor"...

 

"Given That?"  That phrase means the same as "It is a Given" or "It is a fact"

That was a great place to STOP reading.. (Which is what I did... LOL)



#3 caffeine

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Posted 29 June 2016 - 12:28 PM

"Of the 60,705 genic regions, 48,400 (80%) had significant similarity (cutoff at 1 × 10−10) to 11,805 human proteins. For the remaining genic regions, the assignment of putative orthology was based on significant matches to known proteins in cartilaginous fishes, chicken, fugu, zebrafish, and C. intestinalis. In total, the genic regions of the elephant shark assembly contain partial or complete sequences for 14,828 genes. This collection defines a minimal set of elephant shark genes that share strong sequence similarity with known vertebrate genes."

Here, researchers used a DNA library of 14,828 elephant shark genes and compared it to human DNA library which they used a total of 11,805 human genes. Elephant sharks contain only about a total of 17,449 protein coding genes, but researchers only used 84% of those genes (i.e. 14,828) for comparison. Out of the 14,828 shark genes they used, they found an 80% match to that of humans. When they compared the number of match genes to humans with that of bony fishes, they discovered that the similarity was less than that of boneless fishes.

 

 

This is not what the above says at all. This is simply describing how they found the protein-coding genes which show similarity to genes in other vertebrates (or, at least, the 6 other vertebrate genomes looked at in this study). They did not use a total of 11,805 human genes - these were the human genes for which they identified probable matches in the elephant shark genome (the 80% of the 14,828 genes identified). The overwhelming majority of that 80% are shared by all vertebrates. Ony 154 elephant shark genes were found which have orthologs in humans but not teleosts; compared to 107 which have orthologs in teleosts but not in humans. These are only a small proportion on the thousands of genes identified.

 

It's worth noting that the study looks for genes present in mammals and sharks but not teleosts; and in sharks and teleosts but not mammals. It does not look for those present in teleosts and mammals but not sharks. It's not a test of overally similarity.

 

 

Lost in the teleost lineage. In other words, these genes have disappeared in ray-fin/lobe-fin/teleost fishes but appeared earlier in chondrichthyes, which appeared first in the fossil record before the teleost lineage began (i.e. bony fishes) and also in tetrapod vertebrates, which appeared after the teleost lineage. Basically, these missing genes have appeared earlier, disappeared in between, and reappeared again later when tetrapod vertebrates were around even though those genes were even absent in invertebrates.

Sounds strange doesn't it?

 

 

It only sounds strange because you're not thinking in terms of common descent. The genes did not disappear then reappear. They were always present in the ancestors of tetrapods, and were lost in the ancestors of teleosts after the two diverged. I've drawn a crap picture to try and make the point graphically:

 

d9kxo0yo6okh_t.jpg

 


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