Carl Zimmer on Junk DNA and Bad Science Journalism

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If haven't yet listened to Ryan Gregory or Larry Moran (or me) on junk DNA, for the love of God, listen to Carl Zimmer before you ever use that term in a scientific paper, press release, or blog post!

For some reason people like to set junk DNA up as a straw man, and pretend that every discovery of functional non-coding DNA is paradigm-shifting. Don't believe them!

Comments

From my quote of the month post:

"The doubters, [John Mattick] says, “keep regressing to the most orthodox explanation [that the long RNAs are junk]. But they can’t just sit on their intellectual backsides and tell us to prove it.”.

If everyone assumed that what we haven't explored or don't understand is uninteresting, where would science be today. I simply cannot understand why visionary people with hypothesis they would like to test and ideas they'd like to throw out (on the function of "junk DNA/RNA) deserve be trampled into the mud like this. You, T Ryan Gregory and Larry Moran are being reactionary, you are standing in the way of scientific progress and enthusiasm. I for one find that very sad.

SciPhu (not verified) | 09/10/08 | 02:37 AM

We're not being reactionary - we're objecting to the fact that people like John Mattick incorrectly suggest the term junk DNA was coined to describe DNA whose function we simply don't understand.

Even worse, people like Mattick pretend that the idea of functional, non-coding DNA is a novel discovery, and tout every discovery of an enhancer region as refutation of the 'junk DNA hypothesis' (this is exactly what Carl Zimmer was criticizing in the post I linked to).

It is not a novel discovery - we've known about non-coding regulatory sequences for decades, and these were not termed junk DNA, as Ryan has repeatedly documented. Contrary to the media hype, the ENCODE consortium was not the first to discover that human genes have regulatory sequences far away from the regulated genes.

I'd like to see Mattick (or you) come up with a coherent answer to Ryan's onion test if you think we're just sitting on our intellectual backsides.

Mike

Michael White | 09/10/08 | 10:20 AM

I have commented on Carl Zimmer’s post and I made the point that even if the term ”junk” was inaccurate they still discovered a novel function for a piece of DNA previously not ascribed such a, or any, function. Carl Zimmer argues that this is bad science journalism, I would call this nitpicking from the scientific ivory tower.

Ryan’s onion test is a comparison between the genome size of two species. It contains unscientific, unfounded and populist terms like “few people would find it easy to assume that onions require much more DNA than humans do”. This test is descriptive of what I referred to as standing in the way of scientific progress and enthusiasm. I see no need for a "coherent answer" to this test. However, please find below the onion test as used on Stonehenge, a different, but still similar, setting:

Say you are the first to discover Stonehenge. As a scientist you can choose between two approaches: 1) dismiss the stone-formation as a pile of rocks with no significance or 2) try to understand why they are arranged in this peculiar manner. This latter approach would require hypothesis and speculation on possible explanations. Using the onion test on the other hand, you would reach the conclusion that there are bigger piles of rock with no apparent function elsewhere, thus this pile of rock is no different. Consequently, using the onion test you would have stood in the way of scientific progress.

SciPhu (not verified) | 09/10/08 | 13:33 PM

I tried to comment on his article but it never showed up. When I tried to submit it again, Discover's crappy Wordpress install said it was a duplicate comment.

My stance was basically defending ScienceDaily, since he implicated them in Wired screwing it up. ScienceDaily is just reformatting press releases, they got it from Yale just like we did. If Yale researchers doing the work throw around 'junk DNA' colloquially it's hard to fault journalists for using the term too.

So it's easier to berate someone else - that's what pundits do - but it doesn't really advance the cause of clean science journalism.

Hank Campbell | 09/10/08 | 14:16 PM

It contains unscientific, unfounded and populist terms like “few people would find it easy to assume that onions require much more DNA than humans do”.

You're missing the heart of Ryan's test: two different onion species have very different amounts of DNA, and it's not at all plausible that one onion species requires massive amounts of regulatory sequence that another one lacks.

And Carl is not nitpicking (and he's not an academic, and thus not in the ivory tower) - he's pointing out that these people are using the term junk DNA inappropriately in an effort to hype a fairly conventional discovery. Again, as Ryan has documented, junk DNA is not simply a term applied to DNA we know nothing about, and that's the point these science stories are getting wrong. Their knocking a straw man.

Mike

Michael White | 09/10/08 | 14:42 PM

Yale Researchers Find “Junk DNA” May Have Triggered Key Evolutionary Changes in Human Thumb and Foot

If the Assistant Professor of Genetics at Yale and senior author of the study wants to use it the wrong way, it's very, very difficult to blame journalists for not calling BS on him. James Noonan is not going around saying the people who wrote that at Yale misstated him.

If Noonan is complicit in hyping his research for populist appeal we have to ask; how are journalists to know what is hype and what is not without becoming assistant professors in genetics?

Hank Campbell | 09/10/08 | 15:02 PM

OK, true, the researchers themselves should primarily shoulder the blame.

Zimmer says this:

The “Wow! Junk DNA is not junk after all” news hook is a tempting one, but it needs to be resisted. At the very least, science writers need to recall some history.

He says it because this hook has been used too frequently lately, and by this point science journalists should be wary of that particular hook.

Mike

Michael White | 09/10/08 | 16:10 PM

Sure, we did a similar version here, though with less hyperbole. It still had 'junk DNA' in the title.

As you and I have collaborated before on the 'genesis' of these articles, you can see how easy it is to go off the rails but the real problem is that since the term 'junk DNA' has become both ubiquitous and colloquial, if we don't use it, no one's going to read it. And saying 'junk is not junk' is really a compliment and a defense of biology.

I am certain 1000X more people read that Wired story than read Zimmer's blog about it. Even with us helping him out. :)

Hank Campbell | 09/10/08 | 16:43 PM

It's not the fact that it's a colloquial, ubiquitous expression that drives me nuts, it's the fact that people make false arguments when they use the term.

Fine, call it junk, but don't pretend (as SciencePhu did, and as many junk DNA stories imply) that there is a core of hidebound reactionaries who don't understand the latest research and are resisting its results.

I know damn well what an enhancer sequence is, nor do I question the existence of these sequences - in fact my research is based on finding non-coding regulatory DNA! These sequences are discovered routinely in the lab I work in. This is my professional field, and I know what the hell I'm talking about.

The fact that this Yale group pretended that their DNA was previously labeled junk DNA doesn't refute Ryan's onion test (the onion vs. onion one), nor does it refute what the originators of the term junk DNA were claiming.

People can call it junk DNA, but they can't imply that the discovery of an enhancer sequence is paradigm-shifting and still be honest.

Mike

Michael White | 09/11/08 | 20:32 PM

Mike, for the record, I said "reactionary" but I never ever said anything remotely like: "that there is a core of hidebound reactionaries who don't understand the latest research and are resisting its results". I respect and admire the extensive knowledge you, T Ryan Gregory and Larry Moran have in this field. That's partly the reason I find it sad that you run the risk of dismissing potentially exiting research by so rigorously fighting all speculations that this "junk"-DNA may have a function(s). That's all, it has nothing to do with your scientific competence, which I am confident is outstanding, - my arguments are exclusively made towards the defensive approach to science that such an attitude represents.

Sciphu (not verified) | 09/12/08 | 02:36 AM

you run the risk of dismissing potentially exiting research by so rigorously fighting all speculations that this "junk"-DNA may have a function(s).

That's exactly what I mean when I say that people claim Ryan and Larry and I are resistant to new research. Nothing any of us has ever said suggests that nobody's going to find enhancer elements in sequence of currently unknown function. The research in question was not "speculation" that junk DNA may have a function - it was the discovery of an enhancer, something that is fairly routine.

What's absurd (and I know you haven't said this, but Mattick seems to buying into this) is the claim that most of the genome of multi-cellular organisms is functional, made up of regulatory sequence or some other such thing. That's what Ryan's onion vs. onion comparison gets at. The discovery of enhancers in some places in does not refute Ryan's argument. What we know about the biology of gene regulation makes it extremely unlikely that the genome is just chock-full of enhancers crammed into every available space. That doesn't mean we aren't going to find more enhancers, it just means that there will be large regions of the genome where there are no enhancers.

Second, Ryan and Larry have carefully explained that in the past people have used the term 'junk DNA' not to refer to DNA that we simply don't understand, but to refer to specific types of non-functional DNA. Look at what Larry Moran says:

Junk in Your Genome

Transposable Elements: (44% junk)1
DNA transposons: 3%
retrotransposons: 8%
L1 LINES: 16%
other LINES: 4%
SINES: 13%

Pseudogenes (from protein-encoding genes): 1.2% junk

Ribosomal RNA genes: essential 0.05% junk 0.09%

Protein-encoding genes:
transcribed region: essential 1.8% junk (not included above) 7.4%
regulatory sequences: essential 0.6%

Repetitive DNA
α satellite DNA (centromeres)
essential 2.0%
non-essential 1.0%%
telomeres
essential (<1000 kb, insignificant)

Total Essential (so far) 4.5%

Total Junk (so far) 54%

1. A small percentage (<1%) of all transposable elements have acquired a function in the human genome.

Some of those estimates may be revised here and there, but the big picture will remain the same.

This is not just dismissing DNA of unknown function as junk. It's because we do know about this kind of DNA that we call it junk. As Larry notes, some transposable elements have acquired a function, but based on what we know about transposable elements, it's extremely improbable (to say the least) that all or most transposable elements have a function.

That's why I say that people are beating a straw man when they argue that the discovery of an enhancer somehow refutes what Larry and Ryan are saying about junk DNA. It's not the changing definition of junk DNA that people are using that bothers me, it's the incorrect arguments.

I don't resist the discovery of regulatory elements, and I haven't pointed to any stretch of DNA and said 'that piece is 100% junk, there is no way any regulatory sequence will be found there.' We may not know where all of the regulatory sequences are, but based on our fairly thorough knowledge of the biology of transposable elements and regulatory sequences, it is legitimate to say that much of the DNA in our genomes is non-functional.

(BTW, I don't really mean to come off sounding angry, just cantankerous, but that doesn't always work so well in writing.)
Mike

Michael White | 09/12/08 | 10:16 AM

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