Junk DNA Bad, Junk Gene Good

A few weeks ago Carl Zimmer wrote a nice post at The Loom taking science writers to task for leaping at every chance to grab ahold of the “Wow! Junk DNA is not junk after all!” news hook. He correctly pointed out that we’ve known for years that non-coding DNA has lots of function, and so we should not celebrate every new example of functional non-coding DNAs as overturning the conventional wisdom.

I, of course, could not agree more, and his piece said it very well. And I really like Zimmer’s writing – he’s one of the few popular science writers who really conveys a deep understanding of the subtle beauty of evolution.

So it’s with great disappointment that I read Zimmer’s “Now: The Rest of the Genome” in today’s NYT. The hook for this story? “Wow! One gene doesn’t just code for one protein after all!”. The central dogma is dead. Oh my.

Here’s the nut graf:

It turns out, for example, that several different proteins may be produced from a single stretch of DNA. Most of the molecules produced from DNA may not even be proteins, but another chemical known as RNA. The familiar double helix of DNA no longer has a monopoly on heredity. Other molecules clinging to DNA can produce striking differences between two organisms with the same genes. And those molecules can be inherited along with DNA.

Several different proteins can be produced from a single stretch of DNA? No way! Not all transcription is involved in making protein-coding RNAs? Shocking! Identical chromosomes can behave differently because of inherited epigenetic marks? Whoa!

The whole point of Zimmer’s earlier piece was that science journalists need to pay attention to history when they’re pimping a story line:

So, are enhancers an amazing new kind of junk that’s not junk?
Nope. The first reports of enhancers came out in 1981, 27 years ago.

Well, he needs to apply the same standard to himself. Alternative splicing was discovered in the late 1970’s. Non-coding RNAs in the 1980’s. And epigenetic effects were described over 50 years ago, with molecular mechanisms first worked out over 25 years ago.

Yes, new genomic data is providing a more complete description of these phenomena. But for Zimmer to pretend that these new data are reinventing what a gene is is as bad a misrepresentation of science history in the name of a story as anything I’ve seen written about junk DNA.

Science writers play a very important role as honest interpreters of science for the public. But if they don’t present science history accurately, they can’t be taken seriously as authorities on science present.

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Barack Obama – Scientist

Was up working all night, and, as I should have been focusing on my grant, I instead kept trying to figure out just what it was that I was feeling about Obama’s victory. The historical nature of the election brought tears to my eyes – how could it not. And I am already planning a triumphul return to Belgium where I spent a year in cafes defending America against the ill-informed and un-selfaware superiority of Europeans who’ve never been here and believe us to be an incorrigibly stupid, radical and racist nation.

But those were not my primary thoughts. What I came to realize as the night went on is that, for the first time in my life (sorry Bill) I will have complete faith in the person running this country – that we have a serious person in the White House, who approaches problems the way I want them to: deliberately and creatively. He reminds me of the best and brightest of my friends and colleagues. I hadn’t really appreciated it before (his training as a lawyer distracted me) but Obama would have been a fantastic scientist. And because of that I slept soundly last night.

(OK – I would have slept soundly last night had I not been up working on a grant. Now, President Obama, about that NIH budget….)

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November 4, 2008

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Genome Technology: Open access on the rise

The November issue of Genome Technology has an article “Ready or Not, Here Comes Open Access” by Meredith Salisbury on the ascendancy of open access.

I haven’t read it yet (grant due next week) but the cover has what I think is the first picture of the three PLoS founders together:

It’s a nice picure – but they cut off the best part of my t-shirt – where is says “Where Would Jesus Publish?“!!!

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Palin was not talking about Drosophila

Now that I’ve had a chance to look at the blog reactions to the Palin fruit fly idiocy, I’m amazed at how rapidly everyone assumed she was talking about Drosophila. This is because most of the world – including virtually all Drosophila researchers – mistakenly believe that “fruit fly” is the proper common name for members of the genus Drosophila. However the proper common name for Drosophila is vinegar fly or pomace fly. Fruit fly properly refers to members of the family Tephritidae. Now, oddly (and I’m sure accidentally), Palin got it right – the project she was criticizing involved the olive fruit fly (Bactrocera oleae) – a tehpritid.

What I find particularly amusing about this is that I’ve had several conversations in the past few years – usually late nights at the bar at the annual Drosophila meeting – about how we should really get Drosophila researchers to use the correct name. But these conversations always end because we quickly realize that the whole issue is absurd. I mean when would it ever actually matter what common name we use for Drosophila. I mean it’s not like it’s ever going to be at the center of a presidential campaign or anything….

[UPDATE: There’s a great historical discussion of the common name of Drosophila in this essay from Mel Green]

[UPDATE 2: It seems that some people seem to think that I was saying that the fact that Palin was talking about Bactrocera instead of Drosophila makes her comments acceptable. I meant nothing of the sort. Whether she was talking about basic research in Drosophila or applied research in Bactrocera, her mockery of science is dangerous, vile and unacceptable. What I find most repugnant is the utter ignorance McCain and Palin manifest – and the pride they seem to take in it].

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Sarah Palin disses MY fruit fly

As I’m sure many of you have now heard, Sarah Palin delivered her first official “policy speech” in which she pressed for Congress to fully fund the Individuals with Disabilities Education Act (IDEA). To enable Congress to fund this without increasing spending, she returned to McCain-Palin’s favorite enemy – the earmark.

And, following recent M-P tradition, she chose to highlight scientific research as the enemy – in particular the evil fruit fly:

Where does a lot of that earmark money end up anyway? […] You’ve heard about some of these pet projects they really don’t make a whole lot of sense and sometimes these dollars go to projects that have little or nothing to do with the public good. Things like fruit fly research in Paris, France. I kid you not.

I’ll come back later to the absurdity of someone dissing scientific research while purportedly pushing progress for people with disabilities. But it was amazing how rapidly – and proudly – the Drosophila research community started sending around the video of her speech. One of my colleagues wrote:

The noble fly is honored to be the focus of Palin’s venom.  I expect that Caenorhabditis elegans, Saccharomyces cerevisiae and Arabidopsis thaliana are quite upset that they were ignored.

Not so fast. Before the Drosophila community gets too excited, I would like to point out that she was not talking about Drosophila. She was apparently talking about true fruit flies from the family Tephritidae – specifically the olive fruit fly, Bactrocera oleae. Rep. Mike Thompson (D-CA) secured $748,000 to develop methods to eradicate the B. oleae – which has the potential to wreak havoc on the California olive crop. Why France?  Well, some of this money went to a USDA research facility located in France  – which the US government set up in France where B. oleae is already established and can be studied without the risk of escape.

Now it just so happens that my lab studies this fly – not B. oleae, but two of its close relatives B. dorsalis and B. cucurbitae. So all my fine Drosophila friends – YOU are not the target of Sarah Palin’s wrath. I am :-).

And if you really want to piss her off, send a small contribution to help us sequence the Bactrocera oleae genome. Only $50,000 to go….

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What do you think Fox fears most?

President Obama

or

a Tampa-Philadelphia World Series

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Was Jesus Haploid or Diploid?

A study published last week in the Journal of Fish Biology confirmed that an earlier report of parthanogenesis in sharks was not a fluke.

Chapman DD et al. (2008). Parthenogenesis in a large-bodied requiem shark, the blacktip Carcharhinus limbatus. J. Fish Biol. 73(6):1473-1477. (No link – I only link to open access articles).

This is being pegged in the popular press as scientists confirming “virgin birth”. The study’s authors assert that the baby shark is diploid, though I don’t see direct evidence to that effect. Which got me wondering about the following “deep” question: was Jesus haploid or diploid? Has any christian scholar ever pondered this question? I see there’s a Yahoo! answers thread on the topic, but none of the answers are convincing.

The funniest answer to the question is from here:

I always thought the “H” in the common interjection “Jesus H. Christ!” stood for haploid

This reminds of a funny idea of Svante Paabo’s. He wanted to get a piece of one of the relics claimed to be Jesus’s foreskin (apparently there’s one in Croatia). Assuming it is actually the appropriate age, he would then try to PCR out mitochondria – which he should be able to do from a 2,000 year old sample. He would then try to isolate Y-chromosomal DNA – which, given the likely state of preservation of the sample, would fail. Therefore he would have scientific proof that Jesus had a mother but no father. QED. (And it would explain those feminine facial characteristics in all those Renaissance paintings).

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Happy Birthday PLoS Biology

Five years ago today Public Library of Science (PLoS) published the first issue of our first journal – PLoS Biology. It was the first step in our plan to liberate the scientific and medical literature from the needless restrictions on access and use imposed by the subscription based journals.

PLoS Biology 1(1)

PLoS Biology 1(1)

Our goal, as expressed in the founder’s essay written by me, Pat Brown and Harold Varmus, was to “catalyze a revolution in scientific publishing by providing a compelling demonstration of the value and feasibility of open-access publication.”

Five years on our flagship journals – PLoS Biology and PLoS Medicine – are thriving successes. The four community journals that followed (PLoS Genetics, PLoS Computational Biology, PLoS Pathogens and PLoS Neglected Tropical Diseases) are amongst the most respected journals in their fields. Perhaps more importantly, several of the community journals are breaking even, and the others are about to – proving that open access is not just a nice idea – it’s a viable business model. And PLoS One is opening the door to a new approach to publishing – harnessing the power not just of pre-publication reviewers, but of all the people who read articles to make peer review a dynamic and ongoing process.

Honestly, it’s pretty much how we planned it.

Pat Brown and I will have more to say later about the state of PLoS and open access on our 5th anniversary (after I finish the two grants I’m writing), but I just wanted to pause today and take stock of the amazing things PLoS has accomplished, and most of all to say THANK YOU!

Thanks to all of the authors who embraced an upstart publisher because they believed in what we were doing.

Thanks to the academic editors and peer reviewers who’ve help PLoS publish outstanding journals that are well-respected across the globe.

And thanks to the amazing staff we’ve had at PLoS in San Francisco, Cambridge and now Toronto. You have done amazing things and I hope you’re as proud in what you’ve accomplished as we all are in you.

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Where Would Jesus Publish?

What I do with my spare time. (T-shirts available soon).

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