Pharyngula

Remedial reading for big-time scienticians

I don’t understand how this happens. You’ve got a good academic position. You’re bringing in reasonable amounts of grant money. You’re publishing in Nature Genetics and Nature Structural and Molecular Biology. And you don’t even understand the basic concepts in your field of study.

For instance, here’s a press release titled “Cause of genetic disorder found in 'dark matter' of DNA”.

For the first time, scientists have used new technology which analyses the whole genome to find the cause of a genetic disease in what was previously referred to as "junk DNA". Pancreatic agenesis results in babies being born without a pancreas, leaving them with a lifetime of diabetes and problems digesting food. In a breakthrough for genetic research, teams led by the University of Exeter Medical School and Imperial College London found that the condition is most commonly caused by mutations in a newly identified gene regulatory element in a remote part of the genome, which can now be explored thanks to advances in genetic sequencing.

Regulatory elements are not and have never been considered junk DNA. The researchers have identified a regulatory region called PTF1A that has allelic variations that cause a failure of the pancreas to form. That’s really interesting! But then you read what they have to say about it, and they are completely oblivious to the literature on genetic structure and gene regulation. Isn’t that something you’d expect them to have studied thoroughly before even proposing this project?

Or how about this press release, “Un-junking junk DNA”. It’s gotten to the point where I just cringe when I see the phrase “junk DNA” in a press release, because it is a sure sign of flamboyant ignorance to come.

"This study provides answers for a decade-old question in biology," explained principal investigator Gene Yeo, PhD, assistant professor of Cellular and Molecular Medicine, member of the Stem Cell Research Program and Institute for Genomic Medicine at UC San Diego, as well as with National University of Singapore. "When the sequence of the human genome was fully assembled, under a decade ago, we learned that less than 3 percent of the entire genome contains information that encodes for proteins. This posed a difficult problem for genome scientists – what is the other 97 percent doing?"

The role of the rest of the genome was largely a mystery and was thus referred to as "junk DNA." Since then sequencing of other, non-human, genomes has allowed scientists to delineate the sequences in the genome that are remarkably preserved across hundreds of millions of years of evolution. It is widely accepted that this evidence of evolutionary constraint implies that, even without coding for protein, certain segments of the genome are vital for life and development.

So many misconceptions. No, noncoding DNA is not synonymous with junk DNA; junk DNA was not so called because its function was mysterious; it is absolutely no surprise that some regions of the genome are vital, even without coding for proteins — haven’t they heard of tRNA or miRNA? Developmental biologists have been yapping for decades about the importance of the switches that control gene regulation…are we just ignored?

I worry that this is a symptom of a serious rot in science education — that we’re turning out great technicians and masters of the arcane art of grant writing who don’t actually understand biology, and in particular have no perspective on what the questions actually are. They may be excellent middle managers, but the comprehension and vision are lacking.

I have a suggestion. If you’re going to do research that leads you to say anything about junk DNA, I urge you to read carefully one or all of the following books: The Origins of Genome Architecture by Michael Lynch; Fundamentals of Molecular Evolution by Dan Graur and Wen-Hsiung Li; or The Logic of Chance: The Nature and Origin of Biological Evolution by Eugene Koonin. Those aren’t lightweight texts — I wouldn’t assign them to your average undergraduate — but hey, you’re a big-time professional scientist. There’s no excuse for not knowing this stuff.

Comments

  1. […] By PZ Myers […]

  2. #2 jhm
    November 12, 2013

    Dude, I saw a vid wherein your gave a lecture/talk about the various parts of DNA and their relative portions of a whole genome (with an audience participation element involving a large piece of sting or such like). Can you link to this or something similar in written form? Thanks in advance.

  3. #3 Young CC Prof
    November 12, 2013

    I would venture to guess that the problem is not with the scientists, but with the people writing the press releases.

  4. #5 @AmidstScience
    November 13, 2013

    I wonder how much is down to the journalists themselves though (or maybe just naively hope that it is more to them than to the scientists themselves). I remember there was a piece I took part in when I was in College, what I said and what got printed had little in common with each other. For instance, I got asked what the timetable was like – I attempted to convey it was variable and give an example of the shortest day (2hrs of lessons + the afternoon of PE) and the longest day (9-5pm lessons with a lunch break). I also said we were allocated 2hrs of “prep” per day. All that appeared in the article was “[name] studies for staggering 10hrs a day”.

  5. […] Weak statistical standards implicated in scientific irreproducibility (original paper here) The Devolution of the Seas: The Consequences of Oceanic Destruction Our Wasted Opportunity To Solve The Mysteries Of The Brain I’ve Got Whooping Cough. Thanks a Lot, Jenny McCarthy. Remedial reading for big-time scienticians […]

  6. #7 jrkrideau
    Canada
    November 15, 2013

    I suspect the actual scientists are doing one of the following: 1)Trying to throttle the publist,
    2) Drowning their indignation at a local bar,
    3) Pounding their head against a concrete wall.

  7. #8 Jim Thomerson
    November 17, 2013

    I am getting the impression that we are, or soon will be, training molecular geneticists who have never heard of Gregor Mendel.

    I was fortunate that my press releases came back for my comments before they were sent out.

  8. #9 john smith
    November 19, 2013

    The Exeter genetics team is a world leader in islet and carbohydrate metabolism genetics. I think its safe to assume (1) they didn’t write the press release, and (2) you know less about this area of genetics than you think they do about DNA structure.

The site is currently under maintenance and will be back shortly. New comments have been disabled during this time, please check back soon.