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Tuesday, February 10, 2015

Nessa Carey and New Scientist don't understand the junk DNA debate

There's a new book on junk DNA due to be published at the end of March. It's called Junk DNA: A Journey through the Dark Matter of the Genome. The author is someone named Nessa Carey. Here's her bio ....
Nessa Carey has a virology PhD from the University of Edinburgh and is a former Senior Lecturer in Molecular Biology at Imperial College, London. She worked in the biotech and pharmaceutical industry for thirteen years and is now International Director for the UK's leading organisation for technology transfer professionals. She lives in Norfolk and is a Visiting Professor at Imperial College.
Pretty impressive.

Here's how she describes her view of the human genome.
The human genome.

Here's the old model. The genome - our DNA - is vitally important because the genes code for the proteins that are essential for life.

Well yes, that's true. And if you like your ice cream only in vanilla, this may be a good enough description.

But allow your taste buds to wander and some fascinating new flavours may seduce you.

There are lots of situations where two things are genetically identical, but which aren't the same. This is the field of epigenetics, and it tells us that there must be more to us than just our DNA code. The science is weird, heretical and fascinating.

If the genes that code for proteins are so important, why do they comprise only 2% of the human genome? For years, the rest was dismissed as unimportant "junk DNA". But now we know that these neglected regions have a huge range of important functions.

Both epigenetics and junk DNA affect huge amounts of life on earth and have a big impact on human health.

I'm the author of The Epigenetics Revolution and Junk DNA: A Journey Through The Dark Matter Of The Genome, books aimed at a non-specialist readership, which discuss the amazing biology behind so much of life around us.

Go on, dive in. You won't regret it. And you won't think about the world in the same way ever again.
This is not looking good. Anyone who starts with the premise that noncoding DNA might all be junk is clearly way out of their depth in this debate. The claim that epigenetics might explain junk DNA is another dead giveaway. Looks like we're dealing with an amateur.

Fortunately, we don't have to wait for the book to make a decision. She has a website and one of the pages is on Junk DNA - The Basics.

Junk DNA has traditionally been defined by what it isn't. It's the bits of the genome that don't code for the strings of amino acids that form proteins. It was dismissed for a long time as having no function. Which is a pretty classic example of the surprisingly common phenomenon in biology where, if we don't know something, we assume there is nothing to know. Whoops.
"Whoops" is right. This is 2015 and tons of stuff has been written about the definition of junk DNA and the history of the idea. It's pretty clear that Nassa Carey hasn't read any of it. [Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means] [Five Things You Should Know if You Want to Participate in the Junk DNA Debate ]

Fortunately, New Scientist has published a review of the upcoming book: An encyclopaedic guide to the dark genome. Let's see if the reviewer, Linda Geddes, will recognize the problem.
SNOW WHITE, the six-toed cat famously given to Ernest Hemingway by a ship's captain, did not get its extra digit as the result of a freak gene mutation.

In fact, extra fingers and toes in both cats and humans result from alterations in junk DNA – the 98 per cent of the genome that has no genes, doesn't code for proteins, and which was until recently dismissed as, well, junk. In the case of extra digits, a piece of regulatory DNA has mutated, "enhancing" the activity of a gene crucial to the development of hands and feet.
Oh dear. You don't have to read any further. Linda Geddes is as ignorant as Nessa Carey. (Unless by "recent" she means 45 years ago.)
It's a formidable subject, but one that Carey, a former senior lecturer in molecular biology at Imperial College, London, is completely at home with. She does a great job of describing the politics of this controversial field. "At one extreme," she writes, "we have scientists claiming experimental proof is lacking to support sometimes sweeping claims. At the other are those who feel there is a whole generation of scientists (if not more) trapped in an outdated model and unable to see or understand the new order."
I guess I'll have to buy the book in order to find out which category applies to me. I have a sneaky suspicion that I'm not going to be part of the "new order."

There's really no excuse for this. All you have to do is Google "junk DNA" or "noncoding DNA" and it takes you right to the Wikipedia article on Noncoding DNA. If either Nessa Carey or Linda Geddes had done this they would have been much more informed than they appear to be.


I wasn't going to write about this because I was afraid it would give Dan Graur a heart attack. However, I fear that he's going to find out about it anyway so it's not my fault.


Anonymous said...

Larry, I know you are pissed you should be just fix the error on Goggle junk DNA. Google is spelt with GOOGLE NOT DOUBLE G.

Joe Felsenstein said...

The correct professional response to this is "Oy vey!".

I have been telling people that the ENCODE announcement was a big setback to the understanding of molecular evolution, and that it may take us about 10 years to get back to where we were.

Make that 11.

Georgi Marinov said...

How do you write a whole book without ever understanding the difference between junk DNA and noncoding DNA?

Presumably, there are some references in that book and I can't really recall a single case of that error being committed in the professional literature.

And then there is the whole "How do you mess things up so badly in 2015 and the internet age?" question that you asked. Now I just decided to see what Google returns and it's not encouraging - something like 1/3 of the results on the first page are from creationists; but there are still a few good explanations there

Georgi Marinov said...

Also, this was published by Columbia University Press - you would think it would have been sent to at least some reviewers to comment on it. My understanding is that university presses do that before publishing books, I've certainly seen people complaining that they cannot get their books published because of negative reviews

Unknown said...

That's right, Georgi.
These scientists may not be as "amateur" as Dr. Moron thinks.

Piotr Gąsiorowski said...

How do you write a whole book without ever understanding the difference between junk DNA and noncoding DNA?

The author's explanation:

"The number of things that you think you understand, but which turn out to be a bit hazy when you first try to write about them, is frankly astonishing."


"You will write vast quantities of notes that you will not use."

The difference must have been lost with those discarded notes.

Georgi Marinov said...

Well, this is a bit like creationists and their habit of always pointing out their PhDs and other credentials (which serious scientist never do).

Nobody who is not an amateur would post such a thing...

steve oberski said...

The simplest explanation is that the author is dishonest.

Like those "I died and went to heaven and met my sister who I never knew I had and then came back to life" books.

Nullifidian said...

Ed, have you forgotten so readily that Dr. Marinov is one of the people who've been schooling you on junk DNA? Do you really think that he was pointing to the fact that this was published by Columbia University Press as evidence contradicting Moran's assessment of the book's claims?

If you understand nothing else about science, please understand this: arguments to authority cut no ice with scientists. Pointing out that something—however wrongheaded and mistaken—about junk DNA, evolution, or any other aspect of science has been published by a journal or academic press is not evidence that it should be accepted. Of course scientific issues are published by academic publishers. Where else should we publish about science—in the Reader's Digest?

Konrad said...

To be fair, she did not claim that "epigenetics might explain junk DNA". The way she kept switching between these two topics certainly _implies_ that she thinks there's some sort of link between them, but I made it to the end of the quote without being enlightened on what she thinks that link might be.

Steve Watson said...

What's a "technology transfer professional"? Because it doesn't sound like a job that actually produces anything useful.

Diogenes said...

Of course epigenetics and junk DNA are related. They're both buzzwords used by her because she thinks they will increase her sales.

To stupid people, these topics are simple. Epigenetics is Lamarckian inheritance and proof Lamarck was right about giraffes stretching their necks, and it's totes permanent changes. Junk DNA is non coding DNA, so say the magic words "Long dismissed as junk..." and ignore the shelf full of Nobel Prizes handed out to mainstream scientists for finding important functions in non coding DNA since the 1950's, that's sixty (60) f$%&*king years ago, starting with Jacques Monod and Francois Jacob-- ignore the shelf full of Nobel Prizes handed out for the last 60 years, then all you have to do is find an obscure prof somewhere who finds a function in eight (8) base pairs of non coding DNA out of 3.2 BILLION and you call that shit a PARADIGM SHIFT. Dummies, grifters, religious nuts and publicity whores all understand Paradigm Shift = $$$$$. They don't know shit about DNA but they understand $$$.

Mikkel Rumraket Rasmussen said...

This was straight up painful to read. There's a serious fucking problem in molecular biology with these legions of uninformed "geneticists".

Mikkel Rumraket Rasmussen said...

"That's right, Georgi.
These scientists may not be as "amateur" as Dr. Moron thinks."

This is funny coming from the guy who ran away from the previous thread when he couldn't actually defend his views on junk DNA.

Unknown said...

Carey has given an interview with NatureJobs talking about her move from academia to industry (
I doesn't talk about what a "technology transfer professional" is, but I think it's rather obvious. If you look at where a field is at any given point there's the published literature on one hand and there's a body of knowledge that consists of grey literature, things that are in prep, preliminary data and some hands on knowledge. By keeping one foot in academia an industry person gets access to this body of knowledge and this allows them to at least anticipate what is coming up. To give a current example: There are a couple of next next gen sequencing approaches, one of which is the Oxford Nanopore. There is a program under which some labs were given MinIONs to test and we are now seeing the first publications from these labs. But these publications do not represent the full status of knowledge on the technique, because there are quite a few more in the pipeline and the labs that have access along with some that don't are communicating. And that can inform a company like Pfizer on whether they have to look to buying into this technology down the line.

Jonathan Badger said...

Basically people who hammer out licensing agreements between universities and industry. While you can make a fairly convincing argument that things like patents aren't useful and knowledge should be shared freely, while such things exist, somebody has to do it.

Joe Felsenstein said...

... which gives me a perfect opportunity to remind people that molecular biology has been defined as "the practice of biochemistry without a license" (attributed to Erwin Chargaff, 1963).

And of course we evolutionary biologists are always encountering molecular biologists, biochemists, and genomicists who think that they are experts on evolutionary biology, without having acquired any knowledge about its theory or methods. Such as the people who think that the entire genome can be "functional", without incurring any mutational load.

Jonathan Badger said...

Erwin Chargraff once claimed that molecular biology was "the practice of biochemistry without a license"...

Jonathan Badger said...

Ha! Joe beat me to it.

Unknown said...

Well, her definition of epigenetics is as broad as that of junk. Where junk is synonymized with noncoding, epigenetics according to her covers any non-genetic effect on phenotype. The differences in weight of inbread lab rats? Epigenetics! The difference between worker bees and queens? Epigenetics!

Or to quote from her book "whenever two genetically identical individuals are non-identical in any way we can measure, this is epigenetics. When a change in environment has biological consequences that last long after the event has vanished into distant memory, we are seeing an epigenetic effect in action."

When defined that broadly of course epigenetics is everywhere. It's also been around for ages. If epigenetics in this sensu lato in extremo just means "not everything about an organism is genetically predertermined" then it's certainly not shifting any paradigms.

Anonymous said...

I think its entirely possible that most of the genome could be "functional' if it produced contiguous large RNAs ( 100kb etc) that were acting as scaffolds to maintain the epigenetic state of chromatin. But this isn't function the way most of us use the term because it wouldn't be sequence specific (except for reg sequences) and one could delete most of sequence with no effect. Anyone who takes the trouble to think about it will see whats going on. The only reason people are getting their panties in whirl over "function" is because the lack of function of large swaths of the genome has been used as an argument against creationism.
Even 'functional junk DNA' is evidence for evolution, its just must harder to explain why to a non-biologist.

Anonymous said...
This comment has been removed by the author.
Diogenes said...

Jibbers Crabst what a dummy. "whenever two genetically identical individuals are non-identical in any way we can measure, this is epigenetics."

So if you have two identical twins, one lives in New York and one lives in LA, this is epigenetics. Or one goes to the gym, takes steroids and bulks up, and the other gets hit by a car and dies, this is epigenetics.

We need a new term for this shit: fecogenetics. Or would you prefer hypogenetics? Let's vote for the best neologism.

Larry Moran said...

Joe Felsenstein says,

And of course we evolutionary biologists are always encountering molecular biologists, biochemists, and genomicists who think that they are experts on evolutionary biology, without having acquired any knowledge about its theory or methods.

I hear you, and I agree that many of us biochemists don't understand population genetics as well as you do.

Such as the people who think that the entire genome can be "functional", without incurring any mutational load.

On the other hand, I've encountered a very large number of evolutionary biologists who don't understand biochemistry. They completely reject the notion that most of our genome could be junk.

I'm doing my best to educate biochemists but I think your task (educating evolutionary biologists) is going to be even more difficult judging by the last evolutionary biology meeting I attended.

Jonathan Badger said...

It's also part of the problem that "official" evolutionary biologists almost always focus on a tiny fraction of the organisms on earth -- eukaryotes, and more likely than not, metazoans. Genomicists, biochemists, and molecular biologists who study Earth's more representative organisms have to do the evolutionary biology because self-styled evolutionary biologists certainly aren't doing it.

Anonymous said...

"But this isn't function the way most of us use the term because it wouldn't be sequence specific (except for reg sequences) and one could delete most of sequence with no effect"

I do seem to recall a paper maybe even on this blog that showed that epigenetics is able to compensate for about 80% knockout genes and doen't really reveal the function of the knocked-out gene unless you stress the organism

Konrad said...

This is great. As a few more examples, all of nutrition science, psychology, and education science are now just sub-fields of epigenetics. We get to reshuffle entire faculties.

Arlin said...

I agree with Jonathan's point about card-carrying evolutionary biologists (and I'm one of them) having a limited focus. The limitations are not just taxonomic, but also relate to certain topics. I used to work on intron evolution. The topic of intron evolution, for its first 20 years, was dominated by fuzzy thinking and poor attention to hypothesis-testing, because the majority of the players (at least 80%, maybe more?) were practicing without a license. Intron evolution was important to everyone working on gene sequences in eukaryotes, but it didn't seem important to evolutionary biologists. Conversely, "the genetic architecture of complex traits" is a topic dear to the heart of evolutionary biologists, but no one else knows what it means. I don't even know what it means, other than that there is a steady funding stream for people to do quantitative genetics.