Scientists cynical use of "Junk DNA"

By Michael Eisen | Published: September 4, 2008

This blog – like many others I presume – was started to give me a place to vent about a pet peeve. The target of my particular ire is the way that scientists who should know better continue to tout every new paper on the function of non-coding DNA as a new discovery that – GASP – “junk DNA is not really junk afterall“.

The latest example surrounds a paper from my friends and former neighbors Jim Noonan, Shyam Prabhakar and Eddy Rubin published last week Science (I won’t link the paper because it’s not in an open-access journal – another pet peeve…).

Prabhakar et al. Human-specific gain of function in a developmental enhancer. Science 321(5894):1346-50.

The paper reports on a the discovery of a conserved noncoding sequence (named HACNS1) that acts as a developmental enhancer and has evolved extremely rapidly in humans and has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque. It’s a beautiful piece of work that has both intriguing implications for human evolution and will serve as a paradigm for similar studies in the future.

What bothers me is not the paper, but the press release that accompanied it. Here’s the headline and beginning:

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

New Haven, Conn. — Out of the 3 billion genetic letters that spell out the human genome, Yale scientists have found a handful that may have contributed to the evolutionary changes in human limbs that enabled us to manipulate tools and walk upright.Results from a comparative analysis of the human, chimpanzee, rhesus macaque and other genomes reported in the journal Science suggest our evolution may have been driven not only by sequence changes in genes, but by changes in areas of the genome once thought of as “junk DNA.”

So here’s a fascinating observation about genome evolution, and yet they feel compelled to – once again – peg the story on the discovery that there is actually something going on in “areas of the genome once though of as ‘junk DNA'”.

Of course Noonan and colleagues know better. They work on non-coding DNA precisely because they know it is NOT junk. So why, when it’s time to make a pitch to the local press officer, do they fall back on this old bromide? It obviously appeals to writers – who love it when they can pitch a story as overturning orthodoxy. It seems minor, but pegging it this way leads to some really attrocious misrepresentations of current biological knowledge.

Here are some headlines on news stories that followed the press release:

Who Says It’s ‘Junk DNA’? (Hartford Cuorant)

Enjoy Your Opposable Thumb? Thank your “Junk DNA” (Discover Magazine)

and my personal favorite

Meaningless Genetic Code Helped Form Human Hands (Telegraph)

Why is this such a problem? Well, first it’s just WRONG. We’ve known almost since the dawn of the DNA age that not all DNA is protein-coding, and that there are essential functions encoded in non protein-coding DNA. Unfortunately, for initially practical reasons, a disproportionate amount (surely in excess of 90%) of research has focused on protein-coding genes, fostering the faulty impression – amongst scientists as well as science writers – that the ~3% of the human genome that is protein-coding contains > 90% of the function. And it would be great if scientists who, because they work on non-coding DNA are particularly aware that this view is incorrect, would stop promoting it in the popular press.

A second, and less obvious, problem is that this view has played into the hands of the intelligent design crowd. For reasons that baffle me, smart scientists continue to cite the “fact” that much of the human genome is non-functional as evidence against intelligent design. And every time a new study comes out reporting that “junk DNA” is not junk, the ID’ers jump on it as validation of the predictions of ID. It’s hooey of course, but we needn’t give them the opportunity.

So, I am making it my mission to shame everyone who uses the term “junk DNA” or its equivalent when talking about new research on the function of non-coding DNA. And every year I’m going to give out “JUNKY” awards to the most egregious examples. Send me your candidates!

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Open collaboration principles

By Michael Eisen | Published: January 1, 2006

I’ve been trying to figure out exactly what the Open Collaboration Principles agreed to by IBM, HP, Intel and Cisco, and seven research universities (including my own UC Berkeley) is all about. It’s being reported in some places as a new statement of support for open source, but that doesn’t seem right to me. The document is not a model of clarity – there’s more footnote text than document text, but I think this part of the statement clearly states what this is about:

This free & open collaboration principles document is the major underpinning of a policy for handling intellectual property rights arising from software related collaborations between industry and universities under circumstances where the participants intend for the results to be made part of a royalty free public commons (a body of knowledge that can be freely used by the public).

The document, in fact, makes it clear that it isn’t endorsing open source per se, rather it is codifying how companies and universities should handle IP when they want to undertake open source collaborations. What this announcement really strikes me as is a statement by these institutions that Bayh-Dole is an impediment to effective collaborations between industry and academia, and that the university IP demands it inspires make university IP more difficult for companies to work with. This is something I (and others) have been arguing for years, and it’s a positive step that these companies and universities are publicly acknowledging this.

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Science’s culpability in the Hwang Woo Suk affair

By Michael Eisen | Published: December 25, 2005

As willing as I generally am to criticize Science, I was going to give them a pass on the Hawng Woo Suk stem-cell fraud thing, even though his recent Science paper (and possible several others) is looking like the most significant scientific fraud since Piltdown. I’m sure that a post-mortem of the peer review of this paper, and any other of Dr. Hwang’s papers that turn out to be fraudulent, will identify places where more diligent peer-review or better editorial oversight could have caught this fraud earlier. However, elaborate frauds like this are difficult to catch, and it would be wrong to blame Science for these events.

But then I picked up this morning’s New York Times and saw the following section in – Under a Microscope: High-Profile Cases Bring New Scrutiny to Science’s Superstars:

Dr. Donald Kennedy, editor of Science – which is in the process of retracting Dr. Hwang’s paper – said scientists had become far less collegial in the past decade, pushing hard to be first in their field. “There are enormous pressures to be extremely productive and at the top of the heap,” he said.

Fame, scientific prizes and, often, lucrative patents await those who finish first, Dr. Kennedy said, but there is little acclaim for those finishing fifth or sixth. “Scientists want to be recognized like everyone else,” he said.

I love the way he innocently blames this on “scientists”, when Science and Nature are the prime culprits! It is these two powerful journals who have created this “winner take all” system with their voracious pursuit of sexy stories, willingness to rush hot papers to press, and refusal to publish the work of careful, cautious scientists who finish second (let alone fifth or sixth). With such a system, is it all that surprising that some people respond by cutting corners, or in some cases simply cheating?

What IS remarkable is that despite these incentives, the overwhelming majority of scientists are honest and would rather be right than win. Too bad Science doesn’t do a better job of rewarding them.

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Fight Intelligent Design – Publish in PLoS!

By Michael Eisen | Published: December 22, 2005

I wrote this Op-Ed in response to the ongoing battles in Kansas, Georgia and Pennsylvania over ‘intelligent design’. The NYT, LAT, Washington Post and the SF Chronicle turned it down. Time to start a blog!

Now that a federal judge in Pennsylvania has ruled that intelligent design has no place in the classroom, the scientists who rallied to defend evolution will return to academia happy that science has weathered yet another assault. But this battle will not be won in the courtroom. Antipathy toward evolution is the natural consequence of a growing gulf between the scientific community and the public. Until scientists close this gap, much of the public will continue to dismiss Darwin’s theories, and we risk losing the broad public support on which science depends.

Rather than blame public ignorance, scientists must accept responsibility for this distressing trend. We go about our business rarely thinking of the public as an audience for, or interested party in, our work. We speak up when crises occur, but this is not enough. We can and should do more to engage the public on a daily basis, and if we fail to do so, we will face far greater problems than intelligent design being taught in our schools.

I propose a simple solution. We should give the public access to the peer-reviewed scientific journals in which we publish our ideas and discoveries. It is certainly the right thing to do – afterall, the public paid for most of this research, they should be able to see what their tax dollars have produced. But does the public want to read these papers? I believe they do. Many non-scientists whose interest is piqued by science stories in the popular press would love to learn more about the research directly from scientists who carried it out. People facing medical decisions would love to read the most accurate and up to date information about diseases and their treatments. When they do, they will find that much of the scientific literature is surprisingly comprehensible to a lay audience (and much more will be once authors know the public may read their work). And anyone who reads these papers will be left with a better understanding of how science works, and why we believe the things we do.

Unfortunately, the public can not access most scientific journals without paying steep subscription or access fees. Fortunately, scientists do not have to publish in these journals. The last several years have seen the birth and growth of “open access” journals that make their contents freely available to anyone with an Internet connection. These publications invite the public in, and they have responded – downloading, reading and even blogging about scientific articles like never before. Simply by choosing to publish in open access journals, scientists can honor the importance of public access and engage the public directly in their work.

But too many scientists still forgo this opportunity. Young scientists believe that success in their careers depends upon publishing in the ‘best’ (read long-established) journals, while established scientists find the allure of ‘prestige’ journals too difficult to resist. When scientists – many of whose salaries and research labs are funded exclusively by US taxpayers – are unwilling to take simple steps to provide the public access to the research they fund, how can we blame the citizenry for feeling disengaged from science?

It is incumbent upon scientists to change this dynamic. We must ensure that hiring, grant review and tenure committees give heavy weight to efforts (or lack thereof) to engage the public. But more importantly, we all must ask ourselves if that Science or Nature citation is worth furthering the dangerous divide between science and the public?

Non-scientists can help scientists engage as well. Next time you read about some cool new scientific advance, find the paper on which this story is based. If you can’t access it, email the authors and request a copy – and ask them why they didn’t make it available to you in the first place. You’ll be letting them know that the public is interested in what they do, and holding them accountable for their decisions. Maybe next time they will publish in a journal that reaches you.

Posted in open access, science and politics | Comments closed