Thursday, July 28, 2016

You are junk

There's an article about junk DNA in the latest issue of New Scientist (July 27, 2016) [You are junk: Why it’s not your genes that make you human]. I've already discussed the false meme at the beginning of the article [False history and the number of genes: 2016]. Now it's time to look at the main argument.

The subtitle is ...
Genes make proteins make us – that was the received wisdom. But from big brains to opposable thumbs, some of our signature traits could come from elsewhere.
You can see where this is going. You start with a false paradigm, "Genes make proteins make us," then proceed to refute it. This is called "paradigm shafting."1

The author of the New Scientist article, Colin Barras, reports on the "shocking" discovery that humans have about the same number of genes as other species. This discovery, "... threatened to overturn everything we thought about what makes us human." He continues, ...
We’ve only gradually come to grasp the full implications of this discovery. The blueprint for building a human, or indeed any complex creature, lies not only in our genes but in other, neglected parts of our genome. This long-overlooked DNA could have shaped iconic traits such as our upright stance, opposable thumbs, big brains, capacity for language, even our tendency to form monogamous relationships. We might like to think of ourselves as pinnacles of evolution, but actually we are mostly made of junk.
As I said in my previous post, there's nothing new here. We already knew in 2001 that the differences between related species were largely due to differences in how genes were regulated. We already knew that all genes were controlled by regulatory sequences lying outside of the gene. This was not a "neglected part of the genome." It was a well-studied and well-understood part of the genome. It is not junk and no knowledgeable scientist ever thought that it was.

The article continues,
In fact, one group was less surprised by the genome shock. Evolutionary biologists had long thought 100,000 genes would make for a fatally complicated genome. And we now know that genes – the sequences of DNA that code for proteins – account for just 1 or 2 per cent of our genome. For a long time the rest was considered to have no function at all, earning it the dismissive title “junk DNA”. While researchers still argue over how much of it truly is junk (see "What do you mean, junk?"), what’s clear is that this trash hides treasure – bits of DNA that control genes like a conductor directing an orchestra, switching them on and off at different times and in different cells.
Let me emphasize, once again, that there was never, ever, a "long time" when we thought that noncoding DNA had no function at all. That's simply not true and anyone who repeats that myth has not done their homework.

The article mentions several examples where noncoding DNA is involved in regulation (duh!). I don't need to mention all of them—you get the idea. The take-home lesson is that in 2001 we were completely ignorant about genes, genomes, and gene expression but since then we've discovered that some noncoding DNA can be functional. A "paradigm" has been shafted.

Isn't it about time we stopped spreading this ridiculous lie?

Here's an egregious example of how today's science writers are misinforming the general public.
Mattick, who is at the Garvan Institute of Medical Research in Sydney, Australia, thinks that junk DNA controls methylation. He suggests cells might transcribe junk into RNA, molecules typically associated with the process of making proteins (see diagram). But this “non-coding” RNA does something else: it influences when and where DNA methylation occurs.

That’s plausible, says geneticist and evolutionary biologist T. Ryan Gregory at the University of Guelph in Ontario, Canada, and he agrees that non-coding RNA might well be involved in managing methylation.
Of course it's plausible. I learned about functional noncoding RNA when I was an undergraduate in 1964 and I knew of examples of regulatory RNAs when I was a post-doc in 1976. There's nothing new here. (BTW, if you have a gene for a regulatory RNA then, by definition, it is not junk.)

Methylation of DNA is associated with gene expression in mammals. If you have a regulatory RNA molecule that influences gene expression then methylation will be affected and so will histone modification. We've understood this for thirty years—long before the human genome sequence was published. The readers of New Scientist are being given an erroneous view of the current state of knowledge in biochemistry and molecular biology and of the history of the field.


1. Thanks to reader Diogenes who invented the term.

10 comments :

  1. Thanks, I appreciated and enjoyed your concise critic.

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  2. Congrats, Larry.

    So you are pretty much agreing that since Gene expression is regulated by RNAs made by the non coding part of the genome, and gene expression is a regulation mechanism of the differences between related species, the assertion that phenotye changes according to genotype, or macro evolution , is false. LOL.

    You just forgot to mention, that this alone also and still does not define body shape. Many other epigenetic regulation factors mechanisms and instructional codes of various kinds are required.

    In short: The blind watchmaker thesis is BUNK. buuum.

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    Replies
    1. Interesting. So non-coding parts of a genome are not parts of a genotype. Who knew?

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    2. Interesting. So non-coding parts of a genome are not parts of a genotype. Who knew?

      Sigh. Were that the only limitation in his understanding, so well displayed in just three paragraphs.

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    3. Grasso: you are pretty much agreing that since Gene expression is regulated by RNAs made by the non coding part of the genome,

      Yes

      and gene expression is a regulation mechanism of the differences between related species,

      Yes

      the assertion that phenotye changes according to genotype, or macro evolution , is false.

      WT actual F?

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    4. Grasso: Many other epigenetic regulation factors mechanisms and instructional codes of various kinds are required.

      Variations in "epigenetic regulation factors" don't persist over enough generations to explain or drive macroevolution.

      Moreover, epigenetic changes can be the result of changes in the enyzmes that methylate the DNA, or in the DNA sequences that get methylated. They can be the effect, not the cause of changes in allele frequencies.

      "Many other...instructional codes of various kinds are required" Well, no. There's no evidence of any epigenetic "instructional codes" wherein changes could drive macroevolution. (We can ask creationists to define "code", but they won't define it.)

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  3. I've been teaching in High Schools for 14 years and at no point during this time have I ever referred to it as "junk". I've known it isn't junk for a long time so how has New Scientist only just discovered this? Biochemistry isn't my major, I'm an analytical chemist by trade but this fact didn't go unnoticed. I learned about gene expression and regulation back when I was an undergraduate. Catch up New Scientist!

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  4. Replies
    1. It may have escaped your notice that per definition functional non-coding sequences are not considered being junk.

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    2. Thanks for setting me straight, Sparkie.
      Wink, wink..

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