More Recent Comments

Sunday, November 01, 2015

More stupid hype about lncRNAs

I've just posted an article about a group of scientists at UCLA who claimed to have discovered 3,000 new genes in the human genome [3,000 new genes discovered in the human genome - dark matter revealed].

They did no such thing. What they discovered was about 3,000 previously unidentified transcripts expressed at very low levels in human B cells and T cells. They declared that these low-level transcripts are lncRNAs and they assumed that the complementary DNA sequences were genes. Their actual result identifies 3,000 bits of the genome that may or may not turn out to be genes. They are PUTATIVE genes.

None of that deterred Karen Ring who blogs at The Stem Cellar: The Official Blog of CIRM, California's Stem Cell Agency. Her post on this subject [UCLA Scientists Find 3000 New Genes in “Junk DNA” of Immune Stem Cells] begins with ...
Do you remember learning about Junk DNA when you took Biology in high school? The term was used to described 98% of the human genome that doesn’t make up its approximately 22,000 genes. We used to think that Junk DNA didn’t serve a purpose, but that was before we discovered special elements called non-coding RNAs that call Junk DNA their home. But we’re getting ahead of ourselves, so let’s take a step back.
Ugh! No knowledgeable scientist ever said that all noncoding DNA was junk. (Have you heard me say this before?) When are we ever going to succeed in getting that message across to the uninformed?
Genes are sequences of DNA that contain the blueprints for the proteins that make your cells and organs function. Before a gene can become a protein, its transformed into a molecule called an RNA. RNAs contain messages that tell a cell’s machinery what types of protein to make and how many.
That's one kind of gene but it's not a correct definition of "gene."
Now back to “Junk DNA”… scientists thought that because this mass of DNA sequences was never turned into protein, it served no purpose. It turns out that they couldn’t be farther from the facts.
The person who's furthest from the facts is Karen Ring.
There are actually sequences of DNA in our genomes that are blueprints for RNAs that never become proteins. Scientists call them “non-coding” RNAs, and they play very important roles in the body such as replicating DNA and regulating gene expression – deciding which genes are turned on and which are turned off.

Another important function that non-coding RNAs control is cell differentiation, or the maturation of immature cells into adult cells. Differentiation is a complicated process, and because non-coding RNAs are relatively new to the scientific world, we haven’t figured out their exact roles in the differentiation of stem cells into adult cells.
This isn't as egregiously wrong compared as some of the rest of the blog post but let's remember that noncoding RNAs have been known for over 55 years. Is that what she means by "relatively new to the scientific world"?
Scientists are already publishing papers on the role of lncRNAs in the differentiation of stem cells in the brain and heart, and further work in this field will undoubtedly uncover many new and important lncRNA genes. If the pace keeps up, the term “Junk DNA” will need to be retired to the junk yard.
Hmmm ... if you read my earlier post you'll recall that even if all 3,000 transcripts were functional lncRNAs this would only account for about 0.1% of the genome. You would need hundreds of similar studies to make a significant dent in the amount of junk DNA, currently estimated to be 90% of the genome.

Along the way, you would have to refute hundreds of published papers showing that most of our genome is junk. Nobody who understands the debate is going to make the kind of ridiculous claim we see in that blog post.

And no knowledgeable scientist would ever agree with the cartoon she publishes along with her blog post. Only IDiots and unknowledgeable scientists believe that junk proponents (like me) base their arguments on genome ignorance.


John Harshman said...

In fact, the claim that junk DNA is DNA with no known function is quite useful, as it serves to indicate that the person making the claim doesn't know what he/she is talking about. And just about everyone who's ignorant makes that claim. It's a shibboleth.

Larry Moran said...

"Shibboleth"! What a good word.

You are right about the claim. It's safe to assume that anyone who thinks junk DNA is based on lack of knowledge about genome evolution is ignorant. Many of them will also be IDiots.

Konrad said...

The text in the cartoon is "Just because of you don't understand, you can't call us 'Junk'!"

Please tell me I'm missing something deep about deliberate use of incorrect grammar.