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Friday, June 26, 2015

Junk DNA is so last century!

My copy of John Parrington's new book, The Deeper Genome: Why there is more to the human genome than meets the eye, is due to arrive in about three weeks. However, we already have a number of clues about what's in the book [see How the genome lost its junk according to John Parrington]. The excerpt on Amazon [How the genome lost its junk] tells us that Parrington is aware of the controversy surrounding the ENCODE project but comes down on the side of ENCODE.

That view is shared by science writer Claire Ainsworth who wrote a review in New Scientist: Its' so last century.1 Ainsworth is a freelance science writer with a Ph.D. in developmental genetics from Oxford (Oxford, UK). She is co-founder of SciConnect, a company that teaches science communication skills to scientists.

Here's what she says in her review ....
John Parrington is an associate professor in molecular and cellular pharmacology at the University of Oxford. In The Deeper Genome, he provides an elegant, accessible account of the profound and unexpected complexities of the human genome, and shows how many ideas developed in the 20th century are being overturned.

Take DNA. It's no simple linear code, but an intricately wound, 3D structure that coils and uncoils as its genes are read and spliced in myriad ways. Forget genes as discrete, protein-coding "beads on a string": only a tiny fraction of the genome codes for proteins, and anyway, no one knows exactly what a gene is any more.

A key driver of this new view is ENCODE, the Encyclopedia of DNA Elements, which is an ambitious international project to identify the functional parts of the human genome. In 2012, it revealed not only that the protein-coding elements of DNA can overlap, but that the 98 per cent of the genome that used to be labelled inactive "junk" is nothing of the sort. Some of it regulates gene activity, some churns out an array of different kinds of RNA molecules (RNAs for short), some tiny, some large, many of whose functions are hotly debated. Parrington quotes ENCODE scientist Ewan Birney as saying at the time, "It's a jungle in there. It's full of things doing stuff." And that is one of the most apt genome metaphors I've ever read.
People, including science writers, can have different opinions about the validity of the ENCODE results and whether most of our genome is junk. They can also have different opinions about whether many of the ideas developed in the 20th century are still valid. However, I think it's only fair to at least acknowledge that others may have different opinions.

Ainsworth must be aware of the controversy over ENCODE's claim that most of our genome has a function. She could have pointed out that Parrington supports the function side but many prominent scientists support the junk DNA side. She could have noted that there have been several scientific papers published since 2012 that defend the concept of junk DNA—and defend it very well.

A good science journalist can express an opinion on a scientific controversy but good science journalists are obliged to point out to their readers that this is just an opinion and there are many expert scientists who disagree.

The readers of this New Scientist book review will think that ENCODE was the last word on the debate and that's not good science reporting.

1. The title of the online version is "DNA is life's blueprint? No, there's far more to it than that."


Unknown said...

I see that the images on the cover of Parrington's book and in Claire Ainsworth's review both show left-handed DNA...... Not a good start.

Larry Moran said...

Already noted: On the handedness of DNA

judmarc said...

It's full of things doing stuff.

So is a junkheap.

Piotr Gąsiorowski said...

I was going to make the same point. Why should "things doing stuff in the jungle" be a metaphor for functionality?

Diogenes said...

So is a compost heap.

Or a battlefield after a massacre.

Alex SL said...

RNA molecules (RNAs for short)

Somehow this sticks out to me as just weird writing...

Steve Gerrard said...

New Science meets Andy Warhol: it is now just about getting your 15 minutes of fame.

Steve said...

Noticable change in tone from Larry. How polite and courteous the objection to Ainsworth's piece.

Contrast that with the "IDiots dont know shit" (paraphrasing :) of course) reply to the DI.
Give it up, Moran.

Junk DNA is so last century. Just lovin' it.

Sooo, Larry...time to drop your nets and follow Ainsworth. she's callin' you.

Aceofspades said...

The change to a more respectful tone is probably because the discotute are run by a bunch of idiots that make shit up. It's a complete fucking joke the things you people will believe.

judmarc said...

Unknown said...

Tribute acts include individual performers who mimic the songs and style of an artist, such as Elvis impersonators covering the works of Elvis Presley or groups like The Iron Maidens , an all-female band that pays tribute bands to Iron Maiden.

nmanning said...

Mice thrive without 'junk DNA'
20/10/04. By the DOE Joint Genome Institute

Researchers have deleted 3 per cent of the mouse genome, but the mice show no apparent ill effects.

Yup. So last century. The ID crowd still grasps at their straws over this.

Anonymous said...

It's not just ENCODE anymore it is the NIH ROADMAP project. And DNA information isn't just about the DNA sequences but the methylation states which roadmap is starting to track.

For example, the L1 SINE transposons are indicated to help build separate transcriptomes for every neuron! It's not because the L1 SINE DNA sequences are themselves information rich, but their methylation marks carry information beyond the information in the ACGTs sequences.

Graur's dumb idea goes something like this "because a the ACGT sequences are repetitive, the DNA can't be very information bearing." That's about as stupid as saying the VSLI arrays in a computer chip are repetitive, therefore they can't be information bearing.

Graur noticeably avoids mention of things like epigenetic and epiginomic information that is encoded in the DNA by methylation marks, not the ACGT bases themselves.

The methylation marks convey lots of information on "junk DNA", and if we sum all the information in the possible 200 trillion separate transcriptomes for every cell, "junk DNA" might be carrying guadrillions of bits of information -- because it's not in the ACGT sequences alone, it's in the methylation marking patterns that are potentially unique to every cell and that's how a multicellular organism as complex as a human can be managed through development cycle.

And ENCODE and ROADMAP are just scratching the surface. You're advocating the search for function be abandoned before we even look based. I don't think it's wise to appeal to evolutionary biology to describe the physiology and function of cells. I'd think the discipline of molecular and cellular biology and the high throughput techniques of ENCODE and ROADMAP are better ways to settle the issue.

Junk DNA is so last century because it is based on evolutionary theory which was so last 2 centuries.

The whole truth said...

Hey slimy sal, your YEC beliefs are what's really, really antiquated.

"liarsfordarwin" is obviously slimy sal cordova. Read this thread:

Dazz said...

How come this retard is posting entries at Dr. Liddle's blog?

Piotr Gąsiorowski said...

LOL, there are even parallel spelling mistakes: "epiginomic" and "VSLI" in the post above, and:


Sal's fingerprints are all over the place. But it isn't difficult to find out that the weird and rather unsucccessful blog called Liars for Darwin is owned by Sal, so detective work isn't really necessary.