The uncertainty over the results of the ENCODE project culminated in a nasty exchange of words on Twitter last week. Whoever said science wasn’t dramatic!
It’s always exciting to see scientific debates unfurl on your Twitter timeline. Scientists are usually quite well-behaved (online at least) and you don’t usually catch them being nasty. But that was before I spotted the likes of Dr. Dan Graur.
The original theory
The draft sequence of the human genome was published in early 2001. Amongst the Human Genome Project’s (HGP) most fundamental discoveries was that the human genome (the entire genetic material in our cells) consisted of only about 23,000-26,000 genes. This comprises a mere 2% of the entire genome. Since genes are the parts of our genome which direct protein production, and proteins are what keeps us alive, this discovery meant that the rest of our genome, ie. 98% of it has no detectable function. As a result, this 98% came to be called ‘junk DNA’.
Last September, a HGP spin-off project called ENCODE (Encyclopedia of DNA Elements) introduced a twist in the tale. After 5 years of research, hundreds of ENCODE scientists published their results which showed that much of what we perceived as junk DNA since HGP ended is not so at all. In fact, ENCODE identified over 10,000 new genes and claimed that about 80% of our genome has a biochemical function (meaning that the absence of that sequence would affect the cell’s biochemistry) as opposed to the famous 2% that had found its place in textbooks just about a decade ago.
Dr. Ewan Birney, one of the principal investigators of the ENCODE project described the discovery in a nice, balanced self-interview here.
Like any other scientific revelation, the ENCODE findings too went and is going through its share of criticism. Most of the conflict arises out of the lack of clarity around the definition of casually thrown around terms like “function” and “junk.” Is a section X of our genome “functional” only if it is responsible for some observable characteristic in an individual (like blood type, eye colour, height etc.)? Or can section X only affect the biochemistry of the cell and not the entire organism and still be called “functional”?
Similarly, others argued that “junk” DNA never really implied that those stretches of genetic material were completely pointless. We always knew that there were parts of our genome, which despite not being involved in protein production, were crucial as regulatory regions. In other words, many of the non-genes indirectly controlled when genes would switch on and off. So when we already knew this, is ENCODE’s data really as significant as it is made out to be?
The criticism was always there, and ENCODE scientists like Dr. Birney have been quite reasonable and scientific in the manner they tackled their opponents. But then Dr. Graur came along.
Dr. Dan Graur, an evolutionary biologist with Houston University was the lead author of an unusually dramatic research paper published last week titled ‘On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE’. In the abstract of the paper, Dr. Graur claimed that ENCODE’s results were “absurd” owing to largely erroneous methods, inconsistent definition of ‘function’, and statistical exaggeration.
“The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.”
Rather unusually aggressive a tone for a research article. ENCODE supporters and much of the scientific fraternity stood up for Birney and gang.
Dr. Graur didn’t back off though. If you follow him on Twitter you’ll come to realise he probably isn’t known for his gentlemanliness (“Were you born dumb? Or did your mother drop you on your head?” he tweeted to one indignant critic).
Even big names in science journalism joined in.
Birney himself handled the attack impressively.
Even though the vagueness around scientific terminology seems to be hampering a proper understanding of the human genome, the more it is talked about the closer we get to a proper definition. That ENCODE is being scrutinized so much itself can prove to be a good thing for molecular biology in the long run. But this episode is not just about ENCODE.
Big projects involving big money have always been a contentious topic, though traditionally less so in the biological sciences than in physical sciences. Dr. Birney says that the real issue Dr. Graur and gang have is against big science.
Some others are perturbed by the unconventional conduct of Dr. Graur and in awe of Dr. Birney’s composure. While this is an interesting aspect to the drama, I think it’s encouraging that scientists like Dr. Ewan Birney are willing to rise above petty catfights and engage in constructive dialogue with detractors instead of succumbing to the outpouring of support he is receiving from all over.
(Nandita Jayaraj writes about her encounters with the strange and interesting. You can send her feedback at email@example.com. You can also tweet her @nandita_j )