ERVs and Immunity

TIL not to post before I have my first cup of coffee

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I see various problems here. Transcription is not function. If some elements of a large family of sequences have function, that doesn’t mean that all of them do. Most of them could still be junk. Now, if in fact there is evidence that some of these elements show long-term sequence conservation, much more conserved than neutral evolution would show, that’s evidence of function. But what percent of ERVs are conserved?

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Really terrible pop-sci article, and the paper doesn’t seem to be any better. I found no actual evidence in the paper that any of the ERV transcripts identified were actually functional. They do no work to distinguish between pervasive/accidental or functional/selected-effect transcription. They just straight out assume that if it’s transcribed, it’s functional.

Not even a cursory mention of the phenomena of accidental or pervasive transcription are found anywhere, none of the relevant literature is cited, the term junk DNA is found nowhere, and the whole thing seems to be carried by the vacuous blind assertion that:

Whilst EVEs were originally thought to serve no function, as they usually accumulate mutations over millions of years and the majority no longer express functional proteins, a cellular role for some EVE derived RNA or proteins has been identified (Honda and Tomonaga 2016).

Heck, they don’t even describe relative degrees of conservation at the level of sequence to distinguish between things that might or might not be functional.

This was the same fundamental problem with the grandiose ENCODE press releases that accompanied their papers. It’s trash.

But hey, it says this in the acknowledgements:

We thank John Mattick (UNSW) for useful discussion on small RNA.

:laughing: :woman_facepalming: :man_facepalming:

Larry Moran has lots of posts on John Mattick. I think this is the latest: Sandwalk: John Mattick's latest attack on junk DNA

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(Famous as the inventor of the dog’s ass plot.)

Thanks, I appreciate your feedback. This is not my field, so I can’t really evaluate the work. I also appreciate your looking at the original paper. This is very helpful.

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The very first sentence in the article is objectively false.

Please cite the primary literature instead of lazy popularizations like this.

I can’t seem to see the article here. Could you link it?

So it’s ENCODE all over again?

Well, it does share certain features.

I took it down because I posted it without reading the original paper. Apparently, the original paper wasn’t very good. I’ll see if I can find it. But there’s already enough dubious research floating around. I don’t want to contribute to the problem.

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Based on the feedback on the article from forum participants, our friend @stlyankeefan (love the alias!) appears to have withdrawn the link.

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