For more than a decade, Feschotte has pointed to transposons as the ultimate innovators in eukaryotic genomes. Transposons are genetic elements that can copy themselves and insert those copies throughout the genome using a splicing enzyme they make. Feschotte may have finally found the smoking gun he has been looking for: As he and his colleagues recently reported in Science , these jumping genes have fused with other genes nearly 100 times in tetrapods over the past 300 million years, and many of the resulting genetic mashups are likely to encode transcription factors.
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Wonderful paper. I thought for sure I had posted about it when it came out, but apparently I didn’t.
I had the pleasure of hosting a visit from Cedric Feschotte a few years back. He is a fantastic scientist.
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I had read this earlier in the day and thought it was pretty cool. But in general I think transposons continue to be more fascinating the more I learn about them.
But I was completely confused on this makes sense within an evolutionary framework - there was sort of an explanation in the article, but how does a system that complex with cascading factors evolve even with a lot of time? I don’t get it. I mean I feel grateful I can say, “cool God made it” 
but if someone wants to explain it in layman’s terms how that can arise via evolution (I understand selection was mentioned) I’d be interested, 'cause yeah … to me how it works is clever and imaginative.
Scientists may begin to think Oscar the Grouch was quite smart - the junk was treasure after all!
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Maybe this might help?
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Off-topic, but I caught this bit from Quanta magazine article:
Strawman much?
I’ve listened to this on repeat probably over 100 times last year, but I’ve found genetics to be way more complicated and confusing but even more interesting since then.
Watching it now makes me think it’s some kind of tragedy really that evolutionary biology isn’t dominated by creationists. 
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Maybe God just created life with the innate capacity to evolve 
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The confusions that may arise from this study is that people may think that (1) it shows that transposons somehow automatically know how to rewire gene regulation so as to solve the problems that the organism faces, and (2) that the “transposons” involved are not the ones still jumping around, but also all the dead ones that are seen in the genome. And thus that we have accounted for much of the alleged junk in the genome, finding it instead to be magically wise genome-reorganizing machinery.
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Regarding this point, there is a really great new paper looking at the population genomics of TE insertions in Arabidopsis. They find, not surprisingly, that the overwhelming majority of new TE insertions that occur near genes are deleterious, although a few are positively selected.
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Instead of asking for a general explanation, it would be more helpful if you could articulate specific points that you’re confused about. The paper describes how a widespread mechanism (mobile element transposition) facilitates the evolution of new or altered genes.
I’m not sure why your reaction to this is that the results don’t make sense in an evolutionary context.
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There’s some discussion at Sandwalk about how people get these ideas. But it does make one despair for science, because it doesn’t sound as if he considers that a metaphor. If they’re under selection, then why are most of them broken?
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It makes sense is what ever lens you are using to interpret the data.
Evolutionary lens
CONCLUSION
Our findings confirm that exon shuffling is a major evolutionary force generating genetic novelty. We provide evidence that DNA transposons promote exon shuffling by inserting transposase domains in new genomic contexts. This process provides a plausible path for the emergence of several ancient transcription factors with important developmental functions. By illustrating how a transcription factor and its dispersed binding sites can emerge simultaneously from a single transposon family, our results bolster the view that transposons are key players in the evolution of gene regulatory networks.
Design lens.
CONCLUSION
Our findings confirm that exon shuffling is a major design feature generating genetic novelty. We provide evidence that DNA transposons promote exon shuffling by inserting transposase domains in new genomic contexts. This process provides a plausible path for the emergence of several ancient transcription factors with important developmental functions. By illustrating how a transcription factor and its dispersed binding sites can emerge simultaneously from a single transposon family, our results bolster the view that transposons are key players in the differentiation of gene regulatory networks.
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Sorry, no. What design for adaptation produces mostly useless, broken junk? By seeing only the rare advantageous mutations you are missing the real picture.
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The design claim is for exon shuffling and gene regulatory networks. The mostly junk DNA claim is pretty tentative at this point. Whatever junk DNA exists can be the result of mutation with design as a starting point.
I find it hard to believe that word salad was designed, much less the genome of its perpetrator.
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The design hypothesis, like the blob, envelopes a degree of evolutionary biology; but then proceeds to focus attention on setting boundaries to the sufficiency of its explanatory power. After all, that nature requires assistance is the point.
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Transposons are just another type of mutation where one thing is copied and gets inserted elsewhere. Since some transposons can have binding spots for regulatory proteins, they can end up inserting in a location where this binding spot can affect the regulation of nearby genes. While most frequently deleterious, some times this regulation is neutral and is just carried along through generations with no effect, and some times it results in higher fitness.
Yeah unfortunately that doesn’t make sense, as transgenerational “differentiation of gene regulatory networks” is evolution, by definition.
In either case what you are describing is a situation where mutations occur(transpositions), and their probability of propagating successfully through multiple generations are determined by their effect of reproductive success. Calling that a “designed feature” is just to put another label on an intrinsically evolutionary mechanism of the random generation of variation subject to natural selection.
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This is as scientifically meaningful as making a design claim for gravity, the standard model of particle physics, and meteorology. In other words, not at all.
As a Christian, I believe that God designed all that is in the universe. That belief, shared by many, has some relationship with the philosophy of science. Aside from that, however, my belief has nothing to do with transposons or the paper that is under discussion.
I do not wish to elaborate on this any further. If you want to start a new discussion on some purported relationship between transposons and intelligent design, @colewd, please open a new thread.
Best,
Chris
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The section below mostly - “architectures.” As well as the function of introns described here. I guess I don’t see how people look at these processes and make sense of them without a designer. Why/how would molecules act in such precise ways to create new functions? How can selection really work WITHIN a cell like that? Seems if you had 100 million years and molecules within cells randomly doing things that would never happen by chance within that timeframe.
But according to Feschotte’s new study, a transposon can occasionally hop into an intron and change what gets translated. In some of these cases, the protein made by the fusion gene is a mashup of the original product and the transposon’s splicing enzyme (transposase).
Once the fusion protein is created, “it has a ready-made set of potential binding sites scattered all over the genome,” Adelson said, because its transposase part is still drawn to transposons. The more potential binding sites for the fusion protein, the higher the likelihood that it changes gene expression in the cell, potentially giving rise to new functions.
“These aren’t just new genes, but entire new architectures for proteins,” Feschotte said.
Yes, but we’d probably mean very different things by that sentence. So also no? 
I hear you but in this case science is not making claims about the origin of matter, its components or its four forces including gravity.
They are simply offering models of how it works. I think this is equivalent to biology offering a model of cellular reproduction’ or chemistry building a model of how H2O is formed from hydrogen and oxygen.