De-Novo Gene Origination from protogenes.

Incl. intelligent design, belief in divine creation

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Re: De-Novo Gene Origination from protogenes.

#101  Postby Fenrir » Jul 04, 2019 9:03 am

Animavore wrote:It's like when Sean Carroll played a vid from Alan Guth at the WLC debate to confirm Craig was misinterpreting BVG.


And the result will be the same. What would they know they're only the authors. Fundies always know better.
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Re: De-Novo Gene Origination from protogenes.

#102  Postby Spearthrower » Jul 04, 2019 11:10 am

Rumraket wrote:The authors have responded and I got permission to post the following from our email exchange:

The upshot is, your interpretation is correct.

The initial duplication of the 9-nt (Fig. 4C) was almost certainly random. There were five GCA repeats already at the site embedded within any of the 27-nt sequence copies (Fig. 3D). Short repeats are prone to expansion as we well know.

For expansion of a functional AFGP coding region as depicted in Fig. 4F to occur, it had to be driven by natural selection, which was indicated in the figure legend (and in the main text). This is the context for the sentence in question.

The paper structured the description of the evolutionary process by genic component. The section on the formation of AFGP coding sequence containing the sentence in question preceded the section on functionalization. I can see how the location of that sentence could lead to mis-interpretation if one does not consider the multiple components holistically.

The alternate sentence you suggested indeed would make it more clear.


:cheers:



Always the best way to address any concerns about the content of a scientific article: ask the authors. Most scientists are more than happy to respond.
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Re: De-Novo Gene Origination from protogenes.

#103  Postby felltoearth » Jul 04, 2019 11:44 am

Why would you do that when any fuzziness and interpretation serves your cognitive bias?
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Re: De-Novo Gene Origination from protogenes.

#104  Postby Wortfish » Dec 15, 2019 6:36 pm

More junk science from an ignorant "science author" in Nature: https://www.nature.com/articles/d41586-019-03061-x

Although de novo genes remain enigmatic, their existence makes one thing clear: evolution can readily make something from nothing


I wasn't aware that non-coding DNA sequences, the majority of which may be functional and implicated in disease, are "nothing".
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Re: De-Novo Gene Origination from protogenes.

#105  Postby felltoearth » Dec 15, 2019 7:01 pm

Your incredulousness is noted.
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Re: De-Novo Gene Origination from protogenes.

#106  Postby Spearthrower » Dec 16, 2019 3:29 am

Wortfish wrote:More junk science from an ignorant "science author" in Nature: https://www.nature.com/articles/d41586-019-03061-x

Although de novo genes remain enigmatic, their existence makes one thing clear: evolution can readily make something from nothing


I wasn't aware that non-coding DNA sequences, the majority of which may be functional and implicated in disease, are "nothing".



Yeah, you're just intentionally mis-reading it.

That's not clever. It's not cunning. It just looks very much motivated and you'd be laughed at by anyone credible if you tried to exploit this.

But given you've just returned from time away after being caught lying... this is not surprising, is it?
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Re: De-Novo Gene Origination from protogenes.

#107  Postby Wortfish » Dec 26, 2019 1:06 am

Here are two articles that seriously undermine the interpretation of de novo origination:

Non-AUG translation: a new start for protein synthesis in eukaryotes
http://genesdev.cshlp.org/content/31/17/1717.full

Regulated translational bypass of stop codons in yeast.
https://www.ncbi.nlm.nih.gov/pubmed/17187982

The ORF is not as straight forward as it may appear.
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Re: De-Novo Gene Origination from protogenes.

#108  Postby Spearthrower » Dec 26, 2019 8:10 am

Panto Season:

Oh no they don't!
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Re: De-Novo Gene Origination from protogenes.

#109  Postby Rumraket » Dec 27, 2019 1:52 am

Wortfish wrote:Here are two articles that seriously undermine the interpretation of de novo origination:


They don't anywhere.
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Re: De-Novo Gene Origination from protogenes.

#110  Postby Rumraket » Dec 27, 2019 2:05 am

Wortfish wrote:More junk science from an ignorant "science author" in Nature: https://www.nature.com/articles/d41586-019-03061-x

Although de novo genes remain enigmatic, their existence makes one thing clear: evolution can readily make something from nothing


I wasn't aware that non-coding DNA sequences, the majority of which may be functional and implicated in disease, are "nothing".

Even you can't be that dumb that you think the author thinks non-coding DNA is literally nothing.

Also, DNA doesn't need to be functional to be implicated in disease. Nonfunctional and random DNA, if it is not otherwise kept packaged into nucleosomes and therefore transcriptionally silent, will reliably recruit transcription factors even from noncanonical regions only slightly similar to promoter sequences, and produce RNA transcripts that can interfere with normal cellular processes.

Experiments have revealed that much non-coding DNA is often as little as one single base-substitution away from acquiring similarity high enough to a canonical promoter, to start acting as one.
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Re: De-Novo Gene Origination from protogenes.

#111  Postby Spearthrower » Dec 27, 2019 8:38 am

Even you can't be that dumb...


Gonna have to stop you there.




That was it; there was no follow on from that.
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