More Recent Comments

Saturday, January 16, 2016

Brandeis professor demonstrates his ignorance about junk DNA

Judge Starling (Dan Graur) has alerted me to yet another young biologist who hasn't bothered to study the subject of genomes and junk DNA [An Ignorant Assistant Professor at @BrandeisU Explains “Junk DNA”].

This time it's Assistant Professor of Biology Nelson Lau. He studies Piwi proteins and PiRNAs.

Lau was interviewed by Lawrence Goodman, a science communication officer at Brandeis University: DNA dumpster diving. The subject is junk DNA and you will be astonished at how ignorant Nelson Lau is about a subject that's supposed to be important in his work.

How does this happen? Aren't scientists supposed to be up-to-date on the scientific literature before they pass themselves off as experts? How can an Assistant Professor make such blatantly false and misleading statements about his own area of research expertise? Has he never encountered graduate students, post-docs, or mentors who would have corrected his misconceptions?

Here's the introduction to the interview,
Since the 1960s, it's largely been assumed that most of the DNA in the human genome was junk. It didn't encode proteins -- the main activity of our genes-- so it was assumed to serve no purpose. But Assistant Professor of Biology Nelson Lau is among a new generation of scientists questioning that hypothesis. His findings suggest we've been wrong about junk DNA and it may be time for a reappraisal. If we want to understand how our bodies work, we need to start picking through our genetic garbage.

BrandeisNow sat down with Lau to ask him about his research.
There's nothing wrong with being a "new generation" who questions the wisdom of their elders. That's what all scientists are supposed to do.

But there are certain standards that apply. The most important standard is that when you are challenging other experts you'd better be an expert yourself.
First off, what is junk DNA?
About two percent of our genome carries out functions we know about, things like building our bones or keeping the heart beating. What the rest of our DNA does is still a mystery. Twenty years ago, for want of a better term, some scientists decided to call it junk DNA.
Dan has already addressed this response but let me throw in my own two cents.

There was never, ever, a time when knowledgeable scientists said that all 98% of the DNA that wasn't part of a gene was junk. Not today, not twenty years ago (1996), and not 45 years ago.

There has never been at time since the 1960s when all non-gene DNA was a mystery. It certainly isn't a mystery today. If you don't know this then you better do some reading ... quickly. Google could be your friend, Prof. Lau, it will save you from further embarrassment. Search on "junk DNA" and read everything ... not just the entries that you agree with.

I added a bunch of links at the bottom of this post to help you out.
Is it really junk?
There’s two camps in the scientific community, one that believes it doesn’t do anything and another that believes it’s there for a purpose.

And you’re in the second camp?
Yes. It's true that sometimes organisms carry around excess DNA, but usually it is there for a purpose. Perhaps junk DNA has been coopted for a deeper purpose that we have yet to fully unravel.
It is possible that the extra DNA in our genome has an unknown deeper purpose but right now we have more than enough information to be confident that it's junk. You have to refute or discredit all the work that's been done in the past 40 years in order to be in the second camp.

I strongly suspect that Prof. Lau has not done his homework and he doesn't know the Five Things You Should Know if You Want to Participate in the Junk DNA Debate.

What possible "deep purpose" could this DNA have?
Maybe when junk DNA moves to the right place in our DNA, this could cause better or faster evolution. Maybe when junk genes interacts with the non-junk ones, it causes a mutation to occur so humans can better adapt to changes in the environment.
Most of the undergraduates who took my course could easily refute that argument. I'm guessing that undergraduates in biology at Brandeis aren't as smart. Or maybe they're just too complacent to challenge a professor?

We've got a serious problem here folks. There are scientists being hired at respectable universities who aren't keeping up with the scientific literature in their own field. How does this happen? Are there newly hired biology professors who don't understand evolution?

Eddy, S.R. (2012) The C-value paradox, junk DNA and ENCODE. Current Biology, 22:R898. [doi: 10.1016/j.cub.2012.10.002]

Niu, D. K., and Jiang, L. (2012) Can ENCODE tell us how much junk DNA we carry in our genome?. Biochemical and biophysical research communications 430:1340-1343. [doi: 10.1016/j.bbrc.2012.12.074]

Doolittle, W.F. (2013) Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. (USA) published online March 11, 2013. [PubMed] [doi: 10.1073/pnas.1221376110]

Graur, D., Zheng, Y., Price, N., Azevedo, R. B., Zufall, R. A., and Elhaik, E. (2013) On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution published online: February 20, 2013 [doi: 10.1093/gbe/evt028

Eddy, S.R. (2013) The ENCODE project: missteps overshadowing a success. Current Biology, 23:R259-R261. [10.1016/j.cub.2013.03.023]

Hurst, L.D. (2013) Open questions: A logic (or lack thereof) of genome organization. BMC biology, 11:58. [doi:10.1186/1741-7007-11-58]

Kellis, M., Wold, B., Snyder, M.P., Bernstein, B.E., Kundaje, A., Marinov, G.K., Ward, L.D., Birney, E., Crawford, G. E., and Dekker, J. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) 111:6131-6138. [doi: 10.1073/pnas.1318948111]

Morange, M. (2014) Genome as a Multipurpose Structure Built by Evolution. Perspectives in biology and medicine, 57:162-171. [doi: 10.1353/pbm.2014.000]

Palazzo, A.F., and Gregory, T.R. (2014) The Case for Junk DNA. PLoS Genetics, 10:e1004351. [doi: 10.1371/journal.pgen.1004351]


NickM said...

Someone tell him to talk to Doug Theobald, who is at Brandeis...

Eric Falkenstein said...

"There was never, ever, a time when knowledgeable scientists said that all 98% of the DNA that wasn't part of a gene was junk. Not today, not twenty years ago (1996), and not 45 years ago."

"It is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.' Dawkins, The Greatest Show on Earth

98, 95, pretty close. Dawkins does reflect some conventional wisdom, does he not?

colnago80 said...

At this point, some wise advice to Prof. Lau from former US President Truman: If you can't stand the heat, get out of the kitchen.

Larry Moran said...

I deliberately said "knowledgeable scientist" for a reason.

Richard Dawkins is not knowledgeable about genomes but at least he didn't say that if it's not a gene then it's junk.

BTW, the conventional wisdom is that at least 90% of the genome is junk and there are lots of functional sequences that aren't genes.

colnago80 said...

I reread what Prof. Moran and I agree he was a little rough on Prof. Lau. However, I've seen much worse from physicists like Murray GellMann and Julian Schwinger in slapping down colleagues who they conclude don't know what they are talking about (I saw my PhD thesis adviser on the receiving end of such a slap down from the late Prof. Schwinger).

Diogenes said...

What Dawkins wrote doesn't exactly contradict what Larry wrote. Suppose Dawkins were right. The genome is 95% junk and 5% functional. But genes are less than 2%. So *most* functional DNA would still be non-coding.

I'd bet the genome is 8% functional and 92% junk. So Dawkins isn't far off.

Ken M said...

As with "junk DNA", Dr. Moran's post raises poignant questions about the dangers of oversimplifying the controversies of the "junk food" field of research.