The post is from Dec. 1, 2015—that's only one month ago so she should be aware of all the facts concerning junk DNA.
If you are going to write about a subject in your area of expertise then it's reasonable to make yourself informed, especially if you know that the subject is controversial. For some strange reason, this common sense approach seems to be ignored when discussing genomes, evolution, and junk DNA. I don't know why some researchers think they know enough about a subject when all they've done (apparently) is read a few popular press reports.
Let's look at what Bryony Graham (@byrony_g) writes to see whether she is behaving like a proper scientist should behave when writing for the general public. It's worth noting that she was on the shortlist for the 2011 Max Perutz Science Writing Award so somebody must think she's a good science writer.
Not all junk DNA is rubbishActually we DO have a pretty good idea about most of our genome. Thousands of papers on transposons and transposon-related sequences have been published. We know for a fact that about 50% of our genome consists of bits and pieces of defective transposons derived from once active transposons. We know quite a bit about the rate of decay and quite a bit about the transposons that are still active.
It’s because, over a decade after the first draft of the human genome was published, we still really don’t have any idea of what most of it actually does.
We know where transposons sequences come from (SINES and LINES) and we have a good theoretical understanding of why the bits and piece are still in our genome in spite of the fact that they have no function.
There are thousand of papers on introns. They make up about 25% of our genome. We know about their evolution and we know about their sequence conservation, or lack of conservation. We know how introns are spliced out and what sequences are required for that function. We have very good reasons for concluding that the vast majority of intron sequences are unnecessary for a functional gene.
There are thousands of papers on highly repetitive DNA. This includes centromeric regions and telomeres. We know a lot about such sequences and which ones are important.
We know about protein-coding genes and we know about genes for functional RNAs. We know about origins of replication and scaffold attachment regions. We know about regulatory sequences and how much DNA is required for regulation. We know that less than 10% of the human genome sequence is conserved. We know about other genomes and the "C-Value Paradox."
In other words, 15 years after the announcement of the human genome sequence we have a damn good idea about what most of it actually does. It's mostly junk.
One of the most surprising outcomes of the completion of the first draft of the sequence was that there are far fewer genes than anyone anticipated. In fact, genes make up only 2% of the human genome, with the remaining 98% often dismissed as “junk” DNA.It's a myth that knowledgeable scientists2 were surprised to find "only" 30,000 genes in the initial draft sequence.
Genetic load arguments alone yielded an estimate of fewer that 30,000 genes back in the late 1960s. Knowledge of the genes in Drosophila, C. elegans, and yeast led to very accurate estimate of the probable number of genes in humans. Besides, before the draft sequence of the human genome was published we already had the sequence of chromosome 22 (1999) and an extended regions of the MHC locus (1991). Extrapolating from those regions gave estimates of 20,000 - 30,000 genes in the entire genome.
Knowledgeable scientists were very happy when the human genome sequence was published because their predictions turned out to be accurate.
As for the idea that all noncoding DNA was dismissed as junk, this is also a myth. No knowledgeable scientist ever claimed that all noncoding DNA was junk, even 45 years ago. Such scientists would have to have been completely ignorant of genes for functional RNAs, regulatory regions, origins of replication, and centromeres to name just a few of the noncoding functional DNA sequences that were known back then.
It doesn't take much effort to discover that this is a myth. A simple Google search will reveal the truth. But even that shouldn't be necessary. All you have to do is discuss this claim with your colleagues, mentors, and students and pretty soon someone will correct you (I hope). You would think that most scientists in the field would have had such discussions before writing about junk DNA for the general public.
The next surprise came when, after sequencing the genomes of thousands of patients suffering from a variety of genetic disorders, scientists discovered that 88% of changes to the genetic code that correlated with the disease were found in the junk DNA.This statement may be true. It's possible that the experts on genetic diseases were unaware of the importance of regulatory sequences in controlling gene expression. They may have been surprised.
What's not true is that 88% of the mutations causing genetic diseases were found in junk DNA. Many of them are in promoters and enhancers that were never counted as junk. Some of them occur in true junk DNA regions where a new splice site or a new promoter/enhancer is created by mutation. Those regions are still junk DNA. (It's also not true that they are changes in the "genetic code" but that's quibbling.)
The Wellcome Trust has just awarded a £3m grant to the institute where I work, the MRC Weatherall Institute of Molecular Medicine at the University of Oxford, to process samples of DNA from patients known to have a given genetic disease, identify the changes to the DNA which underlie the condition in question, and try and link these changes to genes which may cause the diseases themselves.I think we have a pretty good idea what we're going to find when we identify the mutations that cause genetic diseases. I'm very confident that it won't change the fact that 90% of our genome is junk.
With this strategy, we hope to add functionality to the DNA sequence information, and try to work out what that 98% of junk DNA actually does and how it contributes to disease progression.
The important question here is how did we ever get into a situation where so much misinformation is accepted by people who are supposed to be experts in this field? And how did we get into a situation where healthy skepticism is not a prerequisite to writing about science for the general public?
It seems to be younger scientists who won't take the time to inform themselves about the scientific literature before expressing an opinion on a controversial topic. Why has this become acceptable?
1. Here's what she says on her profile: "My research interests focus on understanding the non-protein coding regions of the genome, or 'junk DNA', using stem cells and red blood cells as experimental systems.
I feel very strongly that effective communication of scientific concepts to non-scientific audiences is critical to research process; providing those involved in policy, education and media with accurate and up-to-date information is essential to achieving maximal impact of scientific research."
2. The only ones who count in such a discussion.