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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
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.
Does it even makes sense to launch into a discussion of orphan genes if what constitutes an orphan genes is mistaken?Mung
April 14, 2014
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Salvador deletes my posts, regardless of their content. He claims to support self-correction, but that only seems to be the case when correction applies to someone else.Mung
April 14, 2014
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To all: I suppose that a good question would be the following one: Is this situation unique of the human genome, or not? IOWs, how many orphans are there in, say, the dog genome, and how many of them would be discarded as random non coding sequences according to the methodology used in that paper?gpuccio
April 14, 2014
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Jehu:
So they have gone from Matzke’s argument that enough sequencing will find the parents to the argument that the orphans do not code for anything.
Obviously. Do you remember the good old Sherlock?: "How often have I said to you that when you have eliminated the impossible (IOWs, that neo darwinism may be wrong :) ), whatever remains, however improbable, must be the truth?"gpuccio
April 14, 2014
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In other words, they have gone from being orphan "deniers" to junk DNA "truthers." LOL.Jehu
April 14, 2014
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Jehu:
It looks like Nelson was right and Matzke was wrong, orphans are here to stay.
Jehu, be fair! Remember that it's easy to be right defending a right theory. Everybody is good at that! Let's give Matze full merit in trying to defend as well as possible a wrong theory. :)gpuccio
April 14, 2014
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It looks like VJ Torley was right and Salvador was wrong.Mung
April 14, 2014
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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.
So they have gone from Matzke's argument that enough sequencing will find the parents to the argument that the orphans do not code for anything.Jehu
April 14, 2014
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Gordon Davisson at #5: The 20-40% figure is just a reference to the percentage of new genes that can be considered as orphan genes in all genomes. That is clear at the beginning of the Tautz paper:
Emergence of new genes via duplication and divergence of existing genes is a well established concept in evolutionary biology (Ohno, 1970; Zhang, 2003; Demuth and Hahn,2009; Kaessmann, 2010). However, with the advent of sequencing of full genomes, it became clear that approximately 20–40% of the identi?ed genes could not be associated with a gene family that was known before. Such genes were originally called ‘orphan’ genes (Dujon, 1996), but later it was suggested to rename them ‘taxonomically restricted genes’ (Wilson et al., 2005). They occur in all domains of life, including bacteria (Wilson et al., 2005, 2007; Yin and Fischer, 2006) and viruses (Yin and Fischer, 2008) and methods have been developed to systematically distinguish them from spurious open reading frames (Wilson et al., 2007).
So, that has nothing to do with the specific case of human orphans. In the case og human genome, 1177 (carefully reviewed orphans) out of about 24000 (original ORFs) would be about 4%, so still lower than the general case. Your discussion about new genes arising from non coding segments is extremely important, but I think it has nothing to do with the 1177 orphans, for which, if I understand well, no homology has been found in other genomes, even in non coding parts (that is exactly part of the argument in that paper). The problem remains: a) either they are non coding segments (and they could be non functional, or functionla, like all non coding segments) or b) they are true protein coding genes that cannot be explained by any neo darwinain model. I suppose that truth is probably a mix of the two. Regarding, instead, new functional genes that arise from non coding segments, that's a very important observation, already proven in a few cases, as you correctly explain. It's also, IMO, one of the strongest arguments for design. I strongly believe that many new functional genes are gradually designed from non coding segments, probably mainly through guided transposon activity, and "released" as functional genes only if and when it is necessary. I have argued in that sense many times here.gpuccio
April 14, 2014
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My bad. Dr. Salvador. Senior Engineer.Mung
April 13, 2014
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Jehu:
Mung, so what? The difference isn’t significant to the discussion.
Fine. Salvador is God.Mung
April 13, 2014
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Matzke was an early orphan denier. According to him, back in 2006, orphans would disappear with enough sequencing.
Clearly, as time goes on, we are finding more and more relatives for the ORFans (in 2003, the number of protein coding ORFans was around 5%#, by 2005 (Wilson et al 2005), it was down to 1.2%. Unfortunately for [Paul] Nelson, we are finding the alleged “missing parents” of the ORFans.
It looks like Nelson was right and Matzke was wrong, orphans are here to stay.Jehu
April 13, 2014
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Mung, so what? The difference isn't significant to the discussion.Jehu
April 13, 2014
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Moose Dr at #3: When an ORF is detected in a genome, it happens very often that no protein has been found that corresponds to the ORF. Protein detection is a much more difficult process than ORF detection at the genome level. The authors of the paper are well aware of that, when they write:
Once a putative protein-coding gene has been entered into the human gene catalogs, there has been no principled way to remove it. Experimental evidence is of no utility in this regard. Although one can demonstrate the validity of protein-coding gene by direct mass-spectrometric evidence of the encoded protein, one cannot prove the invalidity of a putative protein-coding gene by failing to detect the putative protein (which might be expressed at low abundance or in different tissues or at different developmental stages).
Therefore, their argument is not that proteins have not been found (that would invalidate a lot of ORFs in most genomes). Their argument is simply that those 1177 ORFs cannot be explained according to a neo darwinian model. That's very clear in their final conclusion:
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.
Emphasis mine. Now, I have no ides if those ORFs are really protein coding genes or not. However, it is very clear that the only reason why they have been considered non coding is that they cannot be easily explained by a neo darwinian mechanism. I am fully confident, however, that if and when 1177 proteins corresponding to those genes will be found, demonstrating that they are indeed protein coding genes, a darwinian explanation for that will immediately be found :)gpuccio
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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Meanwhile, Salvador, the champion of dissent, deletes dissenting posts from his threads. The deleted materiel: Salvador deletes my posts because he’s a hypocrite who doesn’t care for the truth. What’s good for the goose isn’t good for the gander. 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.
Does it even makes sense to launch into a discussion of orphan genes if what constitutes an orphan genes is mistaken?Mung
April 13, 2014
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Meanwhile, Salvador, the champion of dissent, deletes dissenting posts from his threads. The deleted materiel: Salvador deletes my posts because he’s a hypocrite who doesn’t care for the truth. What’s good for the goose isn’t good for the gander. 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.
Does it even makes sense to launch into a discussion of orphan genes if what constitutes an orphan genes is mistaken?Mung
April 13, 2014
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Meanwhile, Salvador, the champion of dissent, deletes dissenting posts from his threads. The deleted materiel: Salvador deletes my posts because he’s a hypocrite who doesn’t care for the truth. What’s good for the goose isn’t good for the gander! 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.
Does it even makes sense to launch into a discussion of orphan genes if what constitutes an orphan gene is mistaken?Mung
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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Ian Thompson @1:
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??!?
Somebody is lying, of course, hoping that nobody notices the obvious BS.Mapou
April 13, 2014
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I have to agree with Moose here; they aren't trying to shut anything down, just recommending updating the annotations based on additional information. Sequence annotation -- basically, picking out and labeling the interesting bits of the genome -- is a very approximate science at this point. If those 1,177 "genes" are removed from the gene catalog, it doesn't mean they're being censored, just that our "best guess about what they are" is being downgraded. They'll still be in the actual full genome data, and since the annotations are approximate (and everyone knows it), they'll still be reassessed and re-reassessed and... Some will probably be removed from the catalog and re-added and re-removed and re-re-...Gordon Davisson
April 13, 2014
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"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." A valid point. "The point is, it is distressing they’ll just force the evolutionary paradigm and shut down inquiry." I don't see them shutting down inquiry. They seem to want to keep orphans out of the gene databases until a protein is verified. This position should spur exploration into the 1177 to find produced proteins. At least hopefully. "What is there to lose if they aren’t? Nothing." The paper's authors argue exactly the opposite. They suggest that putting genes into the gene database will cause researchers to focus on irrelevant data.Moose Dr
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??!?
If I understand this right (and I should qualify that I'm far from an expert), there are actually two different things contributing to the apparent discrepancy. First, most (/all) of the orphan genes are very very similar to non-protien-coding regions in related species. Thus, new genes can be produced with very little (percentage) change in the DNA sequence. For some examples, take a look at “Recent de novo origin of human protein-coding genes” by David G. Knowles and Aoife McLysaght in Genome Research 2009. 19: 1752-1759 (I happen to have it handy because I cited it in another thread...). It examines three novel genes found in humans but not other primates, and examines the changes that produced them in detail. Specifically, look at part B of figures 2, 3, and 4 -- they give the full DNA sequence for the genes in humans, compared to the syntenic sections of the chimp and macaque monkey genomes. In the first one (the CLLU1 gene, figure 2), the full sequence is 369 bases (including the human start and stop codons), but I count only 8 single-base differences (just over a 2% difference). Note that only one of those was responsible for the change:
The critical mutation that allows the production of a protein is the deletion of an A nucleotide, which is present in both chimp and macaque (indicated by an arrow). This causes a frameshift in human that results in a much longer ORF capable of producing a 121-amino acids-long protein. Both the chimp and macaque sequences have a stop codon after only 42 potential codons.
The other two novel genes are a bit more different (in the last case, the human sequence actually has a 10-base insertion), but they're still pretty similar to the other sequences. The second factor is that (if I understand it right) the 20-40% figure refers to all genes across many species, not the genes in a single species. To see the importance of this, consider a (hopelessly oversimplified and unrealistic) example. Suppose we've sequenced a thousand species, and we found two thousand genes genes shared by all of the species, and that each species also has a single gene that's unique to that species. This means that there are three thousand genes total, and 33% of them are "orphan" genes. But for each individual species, only one of its 2001 genes is an "orphan", which is just 0.05%. Reality, of course, is much more complex and messy than that. But hopefully it illustrates the point...Gordon Davisson
April 13, 2014
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Meanwhile, Salvador, the champion of dissent, deletes dissenting posts from his threads. The deleted materiel: Salvador deletes my posts because he’s a hypocrite who doesn’t care for the truth. What’s good for the goose isn’t good for the gander. 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.
Does it even makes sense to launch into a discussion of orphan genes if what constitutes an orphan genes is mistaken?Mung
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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A more important challenge is to find someone who is honest.Mung
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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Salvador is as young earth creationist. Right Sal? Or are you riding the fence on that as well?Mung
April 13, 2014
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Salvador:
That is why I said the orphans are presumed to code for proteins. We don’t know for sure.
From the DI web page on orphan genes:
1. Do orphan genes encode functional proteins? In many cases there is evidence to suggest that they do. Some are highly conserved, even essential for viability to the organism from which they come. Some are involved in important species-specific or group-specific functions./blockquote>
Mung
April 13, 2014
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scordova:
The point is, it is distressing they’ll just force the evolutionary paradigm and shut down inquiry.
Does anything shut down inquiry like deleting the posts of dissenting opinions?Mung
April 13, 2014
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