A de novo–‘Out of Nowhere’ — Gene

Heya... Very nice site. All the best.... Trikke

VIGE is an abbreviation from GUToB (a general and universal theory of biological variation). GUToB is the alternative biological theory that accounts for all biological observations. It is known that microsatellite DNA and the elements currently known as retroelements (or transposable elements, transposons, IS, or the like) can swap DNA strands and influence gene expression. These elements were specially designed genetic elements to delibrately induce variation in a controlled way in ancient multipurpose genomes. The elements themselves and the genetic mechanisms that made them transpose qualify as genetic redundancy and will therefore whither away rapidly (because selection does not act on these elements). It is no surprise that more and more evo-biologist claim that viruses contributes extensively to evolution. That is because what they believe are the remnants of viruses are NOT what they think they are. Rather these elements have been specially created to induce rapid adaptations and speciation events. Selection is irrelevant. That is what GUToB holds. peter borger

Here's the link: http://www.genetics.org/cgi/reprint/170/4/1945.pdf PaV

Peter: could you give us some more information on these VIGE's? I found, very quickly, this paper. Is this along the lines your describing? PaV

it is known to virologists. peter borger

Peter, I already point to recent published research that found less homology between ORFans and viruses than non-ORFAn genes. So there is no evidence that viruses are a significant source of ORFans. Now you are saying that you have found homologs to ORFans in more complex organisms? How did you do this? Did you perform your own BLAST search? Jehu

"ORFans are defined as ORFs (Open Reading Frames) having no sequence homologs in other genomes." This is how it has been defined. Many orfan genes are found in viruses. Since I don't believe viruses just drop out of the sky, I started to check whether ORFans are really orfans. They are not. Many ORFans are lokated in retroelements or other jumping genetic material found in higher genomes (but that does not count, apparently). It should thus be noted that ORFans are not really orfan genes, but that viruses have their origin in jumping genetic elements. In fact, these elements are not remnants of viruses, but rather ar variation inducing genetic elements (VIGE). Viruses have their origin in VIGEs, not the other way around. Darwinians tend to mix thing up. It's their worldview. It is a bit like the 1% difference between chimp an human. "Everybody" in the field knew it wasn't true. "Everybody" in the field knows ORFans are not really ORFans. peter borger

I disagree. I don't see how genes that appear out of nowhere are a problem for ID. On the other hand, they are not predicted for Darwinism. Remember, Darwinism works only by small gradual changes. Darwinism cannot explain large chunks of information that come out of nowhere. Jehu

Sounds like this is a data point that needs further research before it can be connected to either ID or Darwinism as evidence for either. Patrick

ORFans are defined as ORFs (Open Reading Frames) having no sequence homologs in other genomes. Thus there is no evidence of possible evolution of the ORFan gene. Darwinists, desperate to have an explanation, claimed the future sequencing of genomes would find homologous genes. This did turn out to be the case in many instances but additional sequencing also uncovered more ORFan genes, so that the number of ORFans has continued to increase. Darwinists then argued that the ORFan genes were the product of horizontal gene transfer from a virus. So a BLAST search was done comparing the homology of proteins in ORFan genes to virus genes. It was found that only 2.8% of all microbial ORFans have detectable homologs in viruses, while the percentage of non-ORFans with detectable homologs in viruses is 7.9%, a significantly higher figure. So ORFans are actually less likely to derive from a virus than a non-ORFan. The take away point here is that the assumption that this novel gene in a fruit fly came from a virus can't be taken for granted. Horizontal gene transfer from a virus has not shown to be the source of ORFans in other organisms. Jehu

“or any species’ genome” Doesn’t this sound like a, ‘we have all knowledge of all genes and genomes, so we can say this.’, affirmation?

---Borne I agree that it is a little early for such a statement; but, at the same time, they're saying that nothing matches so far. That's why I said in the original post "that time will tell" whether even transposons can explain this. I sort of suspect that they don't know enough about how transposons work. They seem to attribute it exclusively to viral action. My hunch is that there are certain sites in the genome that are ripe for a reverse transcriptase activity, and that, possibly, eukaryotic genomes are capable of a type of LGT (lateral gene transfer). But, again, "time will tell." PaV

"or any species’ genome" Doesn't this sound like a, 'we have all knowledge of all genes and genomes, so we can say this.', affirmation? It seems a little early in genome research history to say something like that. Borne

Bob--wouldn't they have thought of looking for exon-length sequences? I've never BLASTed anything either, but am just supposing the search engine might be able to handle a search for a subset of the overall gene sequence. Maybe someone out there can answer. PaV

PaV - possibly not if they searched for the whole gene. I must admit that I've never BLASTed a sequence, so I don't know what the usual protocol is. Bob Bob O'H

Also, if the gene came about through exon shuffling, then the individual exons should show homology to other exons. i.e. there is a testable prediction.

---Bob They mention that there is no other such gene known. I suspect they've tried to match sequences with genome sequence banks. I would think that an exon would show up in such a search. PaV

I guess it's worth pointing out that they do have evidence for transposons being involved:

The researchers found that most of these exons had a sequence for a transposable element sitting right next to it.

Also, if the gene came about through exon shuffling, then the individual exons should show homology to other exons. i.e. there is a testable prediction. Bob Bob O'H

PaV, I am glad someone picked up on this article. It sounds to me like an ORFan. Paul Nelson has an interesting power point presentation on ORFan from a few years back. I have tried to follow ORFan research since then but it seems like it has trailed off and gone nowhere. The article had this interesting tid bit as well,

scientists ... are discovering that many of the most recently formed functional genes in any species also are expressed in male testes and appear related to spermatogenesis.

So spermatogenesis is a common location of unique genes? Jehu

The information could be more damning than supportive though no matter what it is, it will be considered supportive of gradualism. This information seems to support Behe's EOE hypothesis. If in fact this gene did arise by natural means of shuffling genomic parts around, it is the only gene they can point to in the biological world. Where are all the other unique genes one would expect if NDE was operating as envisioned. They should be a dime a dozen but we only have one. What gives? While I am sure that the gradualist spin merchants are out preparing the hype for this, where are the several thousand other examples that should be available for analysis if NDE was doing its job. jerry