“Groundbreaking” ‘Duon’ Paper Only Continues Research From Prior Studies

There is a lot of chatter on the internets about the press release from the University of Washington about a paper published in the journal Science this week. One claim within the press release is that findings in the present study uncover a ‘hidden’ code within human DNA that scientists had no prior knowledge of. As many have written, this assumption is completely false and grossly exagerated.

After reading the paper (paywall), I can say the study does add a wealth of new information to an already known phenomenon. I recommend reading the article if one is in the molecular biology or human genetics fields. However, the press release about this study should be retracted for the amount of misleading claims raised within it.

In fact, the authors write in the final paragraph,

Our results indicate that simultaneous encoding of amino acid and regulatory information within exons is a major functional feature of complex genomes. The information architecture of the received genetic code is optimized for superimposition of additional information (3435), and this intrinsic flexibility has been extensively exploited by natural selection. Although TF binding within exons may serve multiple functional roles, our analyses above is agnostic to these roles, which may be complex (36).

Pay close attention to the parenthetical numbers within the quote. These indicate the statement is referencing a prior publication. 34 is reference to a paper from 2007 in Genome Research entitled, “The genetic code is nearly optimal for allowing additional information within protein-coding sequences.” and can be found here. 35 is a paper from 2010 also in Genome Research; “Overlapping codes within protein-coding sequences.” found here. And 36 is from Nature Genetics earlier this year entitled, “DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements” found here.

A question for UW Today,

If these authors uncovered an unknown, hidden code within DNA, how could they reference earlier studies that essentially elaborated upon these same ‘secrets’?

I’ll be waiting for an answer…

Repeat after me: There is no newly discovered hidden code in DNA.

It is a very sad and unfortunate occurrence when newly released research findings are hyped and overstated. This week the University of Washington Office of News & Information released a press release embarrassingly called “Scientists discover double meaning in genetic code“. Since then, the release has been picked up by websites across the globe. In that way, the press release did its job. Unfortunately, the statements within the release along with the title have done a world of harm. I can only hope it was unintended.

The release starts by stating scientists discovered a second code hiding within DNA.

This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

This ‘second code’ will not change anything scientists do regarding studying DNA. This ‘hidden second code’ has been known and studied for decades.

Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.

Let me rewrite this paragraph to make it factual:

Since the genetic code was deciphered in the 1950s, scientists have continued to find additional layers of complexity in the regulation of how genes are transcribed to make proteins. The current study from UW scientists have added additional knowledge to this growing field.

This is the most unfortunate part:

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

This release was written by writers in a news department as a marketing piece, but when the scientist also grossly exaggerates the findings, it is very sad. Like Emily Willingham said in Forbes, “I can only hope that Stamatoyanopoulos didn’t really say that”. Scientists have not made any such assumption and have decades of evidence to the contrary.

The study shows that changes in the DNA sequence can have two-fold consequences upon the protein made from it. It can change the amino acid sequence of the protein and change which proteins bind that help transcribe the DNA into the RNA used to create the protein. This is not new. The finding that made this study worth of the prestige of publishing into Science is the frequency of the DNA code that is used to determine which proteins bind to the DNA to create the right form of the protein. These proteins, known as transcription factors, have been known for decades and bind to a number of DNA sequences to ensure the cell creates the exact protein needed.

As is common in press releases, the last part of the piece tries to explain DNA and the language of genes. In this aspect, the release does an even worse job:

The genetic code uses a 64-letter alphabet called codons.

The genetic code uses 64 different combinations of nucleotide sets of three, called codons; most of which code for one of the twenty amino acids needed to make a protein.

I could keep going, but I’m exhausted by trying to set the record straight.

Never send for whom the budget tolls, it tolls for thee: an open letter Part III.

During the current political environment, R&D budgets are being reduced or frozen. For example, the budget for NIH, the largest public funding program in the U.S., is lower than it was in 2003. The “Plan B” outlined in the Budget Control Act of 2011 (aka sequester) plus the current 6-month continuing resolution cycle employed by Congress has all in the research community scared; not only for their own jobs but also for what it is saying to our citizens and people across the globe.  Our ‘leaders’ in Washington no longer consider basic research a priority. In essence, the ‘leaders’ are saying, “We are too worried about our re-election bids to see the big picture and the catastrophic consequences of our short-sightedness”.

The innovations and technologies directly or indirectly resulting from basic research have brought invaluable prosperity to this country and has enriched the lives of each of us directly. Cuts to research are the essentially the same as cuts to flesh. Eventually, the infection at the cut spreads to the entire body. The cut doesn’t suffer, the body suffers. John Donne said it well in his passage, Meditation 17 Devotions Upon Emergent Occasions:

No man is an island,  entire of itself; every man is a piece of the continent, a part of the main; if a clod be washed away by the sea, Europe is the less, as well as if a promontory were, as well as if a manor of thy friend’s or of thine own were;  any man’s death diminishes me, because I am involved in mankind, and therefore never send to know for whom the bell tolls; it tolls for thee.

The bell is tolling in the U.S. and has for some time now. We all suffer when ignoring our research community.

 

Sincerely,

Matt Russell, Ph.D.

Never send for whom the budget tolls, it tolls for thee: an open letter Part II.

The sixty years between World War II and September 11, 2001 were unparalleled for discovery and innovation even though they were fueled by fear. First, fear of Japan, Germany, and later Russia. After the war was over, a new ominous threat emerged that (in the eyes of most) threatened our future as a country if not defeated, communism. ‘Necessity breeds invention’ sure was true during the Cold War and our Research & Development infrastructure became the envy of other countries.

On the tragic day 2,977 innocent lives died, our nation changed. We awoke to a new, hidden enemy with no country boundaries. It brought us together like nothing before. We were united. But some quickly turned to ideology and misinformation leading us into constant military offenses with no real way to fund them. One of the first schemes was by increasing the maximum allowable interest rate of student loans. Personally, mine went from 2% to 6% overnight.

science funding
R&D spending initially rose after 2001. However, this is due to mostly an increase in Defense Department R&D budget increases.

Later on, other sources were needed to continue funding war campaigns. Although most of this funding was borrowed against our future generations, the rest came from discretionary spending. One of the major spending bills is that for science R&D and energy R&D. When the Human Genome Project was completed in April 2003, America’s largest scientific spending project in history was over. Instead of using these funds for other science and technology programs, no other big science project has ever come to fruition (the Spallation Neutron Source began construction prior to 9-11-01).

Never send to know for whom the budget tolls, it tolls for thee: an open letter Part I.

To whom it may concern,

This letter is for any and all that have a genuine interest in the future of our country. Many whose livelihood and passion dwells under the umbrella of Research & Development have watched helplessly over the past decade a deterioration in the enterprise that has made the United States the most successful global leader in the history of civilization. This enterprise emerged from one of the darkest tragedies in our nation’s history on December 7, 1941. With great foresight, our leaders knew resilience and ultimately the preservation of our way of life depended not upon naive belief but creativity and innovation among the brightest minds in the country; themselves immigrants brought here by persecution. 

Beginning with the Manhattan Project, the U.S. has built unchallenged scientific leadership. The unfortunate irony is that another dark tragedy on September 11, 2001 started its slow downward spiral. 

What do you say when #sequester eliminates your position?

Sequester (my adorable princess) is a very misguided attempt to do what's best for science and innovation (adorable baby goat).
A fine line between hugging and strangling. Sequester (my adorable princess) is a very misguided attempt to do what’s best for science and innovation (adorable baby goat).

Warning: this will be a personal post with not much in the way of explaining scientific wonders.

 

I had just graduated with my Ph.D. and was in the job market; ready for an exciting post-doc or a faculty position at a local community college. Full of ideas and enthusiasm, I was going to conquer the world and provide for my family. Little did I know Science had another idea. I applied instinctively for a Research Associate III position. “Science Writer? Hmm, sure, why not?” I thought. They wanted a writing sample based upon a recent journal article. I got a call for an interview and happily scheduled it in my calendar.

I was still on the research/post-doc bandwagon and didn’t think much of the science writer interview until I sat in that chair and talked for an hour about science. It opened my eyes to a whole other world. A world filled not with test tubes and media bottles but with a computer and an imagination. A long term goal of promoting science to anyone who cared to listen soon became a reality when I was offered the position. “You want to pay me how much? I would do it for free!” I thought.

I settled into my new home, an actual office with a window and two computer screens. I was living the American dream. I was studying up on previous documents the group had published; top quality, award winning documents. While waiting for my first assignment, I started a blog to tell the world all the wonderful science discoveries I was taking note of. The group was going through an usual dry spell. “Don’t worry, it will pick up” I was told. It was fall and we should have some meeting documents to work on first of the year (2013).

Thanks to the failure to reach a compromise in response to the Budget Control Act of 2011, budget sequestration took affect January 1, 2013. Austerity had reached American shores and it wasn’t pretty for science and innovation. No new programs could be organized and the forward-thinking science program managers were handcuffed to politics. “It won’t affect me” I thought. Operating on a continuing resolution also meant no new monies for programs…strike two. Thanks to the GSA ‘training sessions’ in lavish resorts, travel restrictions were placed across all federal agencies…strike three.

On August 13, 2013, I was told my position was being eliminated due to lack of work. My wife had just taken a administrative leave without pay from her position because we were days away from becoming foster parents. We also had just found out she was pregnant after a year of trying, including one (maybe two) miscarriages.

 

Sigh…

If you need a face to put with sequester, try my four year old’s.

A story about a political insider and his experience in jail for protesting the Keystone XL Pipeline. A must read…

A presidential adviser, radicalized by American inaction on climate change | MinnPost.