Sunday, April 06, 2014

The American Society of Plant Biologists embarrasses itself by publishing "New functions for 'junk' DNA?"

Theme Genomes & Junk DNAThe American Society of Plant Biologists has put out a press release with the title New functions for 'junk' DNA?.
Non-coding DNA sequences found in all plants may have undiscovered roles in basic plant development and response to the environment.

DNA is the molecule that encodes the genetic instructions enabling a cell to produce the thousands of proteins it typically needs. The linear sequence of the A, T, C, and G bases in what is called coding DNA determines the particular protein that a short segment of DNA, known as a gene, will encode. But in many organisms, there is much more DNA in a cell than is needed to code for all the necessary proteins. This non-coding DNA was often referred to as "junk" DNA because it seemed unnecessary. But in retrospect, we did not yet understand the function of these seemingly unnecessary DNA sequences.

We now know that non-coding DNA can have important functions other than encoding proteins. Many non-coding sequences produce RNA molecules that regulate gene expression by turning them on and off. Others contain enhancer or inhibitory elements. Recent work by the international ENCODE (Encyclopedia of DNA Elements) Project (1, 2) suggested that a large percentage of non-coding DNA, which makes up an estimated 95% of the human genome, has a function in gene regulation. Thus, it is premature to say that "junk" DNA does not have a function—we just need to find out what it is!
I've sent a link to this post to Tyrone Spady [tspady@aspb.org] who is listed as the contact person at The American Society of Plant Biologists and to Gregory Bertoni [gbertoni@aspb.org] who is listed as Science Editor, The Plant Cell.

I'll keep it simple for them.
  1. "This non-coding DNA was often referred to as "junk" DNA ..." No reputable group of scientists ever said that all non-coding DNA is junk. No scientist who understands genomes would ever say that today. [Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means]
  2. "We now know that non-coding DNA can have important functions other than encoding proteins." We have known that for fifty years. Is that what American plant biologists think of as a recent discovery worthy of mention in a 2014 press release? [What's in Your Genome?]
  3. "Recent work by the international ENCODE (Encyclopedia of DNA Elements) Project (1, 2) suggested that a large percentage of non-coding DNA, which makes up an estimated 95% of the human genome, has a function in gene regulation." It is true that the ENCODE Consortium claimed that most of our genome is functional. However, good scientists know that this claim is disputed and the best scientists know that it is wrong. Where does that leave American plant biologists? [Science still doesn't get it] [Ford Doolittle's Critique of ENCODE ]
  4. "Thus, it is premature to say that "junk" DNA does not have a function—we just need to find out what it is!" There is abundant evidence that most of that extra DNA in our genome really is junk. It is not some mysterious black box as you imply. [Non-Darwinian Evolution in 1969: The Case for Junk DNA ] [Five Things You Should Know if You Want to Participate in the Junk DNA Debate]
It's bad enough having to teach biology to creationists but when you also have to teach it to biologists, you know we're in big trouble.


3 comments :

  1. How ironic! They must not be reading the botanical literature, where they're finding many plant genomes replete with junky LTR retrotransposons.

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  2. They publish "Plant Physiology". How depressing.

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  3. Actually, I've read somewhere that even ENCODE scientists claim they were misunderstood...

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