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1,177 human orphan genes removed by evolutionists from databases

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Here is a case of evolutionary bias causing misrecognition of orphan genes in humans. Orphan genes are presumed protein coding genes that exist in only one species and have such non-similarity to anything in any other species they are called orphans (a play on words of the ORF acroym for Open Reading Frame).

This came up in the Nelson-Velasco debate where Velasco said there are 0 orphan genes, and Nelson pointed out the reason some say they are zero is because of their biases.

Nelson has been vindicated as I pointed out in New Mechanism of Evouion — POOF

Here’s is the proof of this cover up Distinguishing protein-coding and noncoding genes in the human genome:

1. “The remaining 1,177 cases were declared to be orphans, because they lack orthology, paralogy, or homology to known genes and are not obvious artifacts… If the orphans represent valid human protein-coding genes, we would have to conclude that the vast majority of the orphans were born after the divergence from chimpanzee. Such a model would require a prodigious rate of gene birth in mammalian lineages and a ferocious rate of gene death erasing the huge number of genes born before the divergence from chimpanzee. We reject such a model as wholly implausible. We thus conclude that the vast majority of orphans are simply randomly occurring ORFs that do not represent protein-coding genes… We found… 12 reported cases of orphans with experimental evidence for an encoded protein”

The problem with these authors is in 2007 they didn’t invoke the POOF mechanism of evolution which other evolutionists happily embrace now in 2013:

However, with the advent of sequencing of full genomes, it became clear that approximately 20–40% of the identified genes could not be associated with a gene family that was known before. Such genes were originally called ‘orphan’ genes

Evolutionary Origin of Orphan Genes

20-40% of the genes discovered cannot be explained by common ancestry or common descent. So what mechanism is left to explain it? Special creation? But evolutionists can’t accept special creation, so they just pretend they’ve made a discovery of a new mechanism of evolution that can work just as well.

They haven’t given it a name yet, so let us call it POOF. What is POOF? POOF is the mechanism by which proteins can easily arise out random nucleotide sequences like a poem can emerge out of randomly tossed scrabble letters. I bold one of their euphemisms for the POOF mechanism in the following paragraph:

Orphan genes may have played key roles in generating lineage specific adaptations and could be a continuous source of evolutionary novelties. Their existence suggests that functional ribonucleic acids (RNAs) and proteins can relatively easily arise out of random nucleotide sequences, although these processes still need to be experimentally explored.

😯

The reasoning they use goes like this, “we have all these genes that can’t be explained by slight successive modifications, so they must have arisen spontaneously out of nowhere. Because evolution is fact, this implies evolution can just take random material and create functional systems in a flash. We’ve made a fabulous discovery about the miracles of evolution even though we can’t demonstrate it experimentally.”

HT JoeCoder
www.reddit.com/r/creation

Comments
One of the challenges is that certain proteins may be expressed only in certain stages of development and some only under environmental stress or other specialized conditions. That is why I said the orphans are presumed to code for proteins. We don't know for sure. The point is, it is distressing they'll just force the evolutionary paradigm and shut down inquiry. What is there to lose if they are really orphans? A lot. What is there to lose if they aren't? Nothing. Thus to me, the 2007 paper symbolizes an attitude that is bad for science. The 2013 paper symbolizes a more open view.scordova
April 13, 2014
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Its interesting when you read the linked material, rather than accepting the interpretation. If I understand the article correctly, when human DNA is searched for the "start code" (ORF) a total of 1177 orphan (non-homologous ORF) cases are found. However, specific proteins produced from those orfs are not detected. This report does not seem to present a fresh experiment to find the proteins associated with these orphans. However it reports that twelve such proteins are reported in the literature. Their argument seems to be that the digital detection of an orphan means little, that the second step of detecting that the orphan actually produces a protein is called for. I don't find their case unreasonable. I think it important to understand how many true protein-coding orphans there are. What is clear is that there hasn't been a search for a matching protein in all 1177 cases of orphans. So the orphan count is likely to climb to much higher than the mathematically impossible 12.Moose Dr
April 13, 2014
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Moose Dr, The point is that none of them agree with Salvador's definition! Have you noticed that Salvador deletes my posts? If he has nothing to fear from the truth, why would he do that?Mung
April 13, 2014
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Mung, I am confused. You present three definitions for an orphan gene. To my layman's eye, all three are substantially the same. So what's your point?Moose Dr
April 13, 2014
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Does it even makes sense to launch into a discussion of orphan genes if what constitutes an orphan genes is mistaken? I think not.Mung
April 13, 2014
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Salvador:
Orphan genes are presumed protein coding genes that exist in only one species and have such non-similarity to anything in any other species they are called orphans (a play on words of the ORF acroym for Open Reading Frame).
No, Sal, that's not what an orphan gene is. Here's the link to the Wikipedia article. Here's how the Discovery Institute defines them:
orphan genes (protein-coding sequences without known protein-coding antecedents)
And there's this:
Orphan genes are protein-coding regions that have no recognizable homolog in distantly related species.
Mung
April 13, 2014
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Salvador claims to be in favor of a self-correcting community. He whines when he receives abuse for disagreeing with ID. So why does he delete posts which expose his ignorance?Mung
April 13, 2014
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Remind me again! how the following two claims are consistent: 1. Chimps, Humans 96 Percent the Same, Gene Study Finds, and 2. 20–40% of the identified genes could not be associated with a gene family that was known before (Tautz et al above) What in heaven's name is going on??!?Ian Thompson
April 13, 2014
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