This was one of those stories this past week that so many people brought to my attention, I had to blog about it. The trouble is, when I read the story, I initially had a rather tepid reaction. Indeed, I had to wonder why so many people found the story intriguing, and in the process, I "reverse engineered" a putative process of reasoning that might have been at work in their fascination with the article. So, with thanks to all who sent in various versions of this story, let's look at two of them:
Just a glance at the titles is, I suspect, reason enough to appreciate why so many people thought this was an intriguing article; both titles state that a completely new structure of DNA has been found, or, in the second article's case, it's the first time it's been seen. And that raises all sorts of high octane speculation possibilities, which we'll get back to presently.
A glance at the first article outlines the basic history behind the story:
In a world first, Australian researchers have identified a new DNA structure -- called the i-motif -- inside cells. A twisted 'knot' of DNA, the i-motif has never before been directly seen inside living cells.
The new findings, from the Garvan Institute of Medical Research, are published today in the leading journal Nature Chemistry.
Deep inside the cells in our body lies our DNA. The information in the DNA code -- all 6 billion A, C, G and T letters -- provides precise instructions for how our bodies are built, and how they work.
The iconic 'double helix' shape of DNA has captured the public imagination since 1953, when James Watson and Francis Crick famously uncovered the structure of DNA. However, it's now known that short stretches of DNA can exist in other shapes, in the laboratory at least -- and scientists suspect that these different shapes might play an important role in how and when the DNA code is 'read'.
"The i-motif is a four-stranded 'knot' of DNA," says Associate Professor Marcel Dinger (Head, Kinghorn Centre for Clinical Genomics, Garvan),.who co-led the research with A/Prof Christ.
"In the knot structure, C letters on the same strand of DNA bind to each other -- so this is very different from a double helix, where 'letters' on opposite strands recognise each other, and where Cs bind to Gs [guanines]." (Emphasis added)
And here's the second article, explaining that structural and binding change:
The fact that scientists finally observed this different form of DNA in human cells is a pretty big deal, but it’s actually even more than just a different shape. It seems to play by different rules than double-helix DNA, too. It employs nucleotides — the basic A, G, T, and C units that compose DNA — a lot differently than helical DNA does.
“The i-motif is a four-stranded ‘knot’ of DNA,” Marcel Dinger, Ph.D., an associate professor at Garvan and one of the study’s authors, explained in a statement released Monday. “In the knot structure, C letters on the same strand of DNA bind to each other — so this is very different from a double helix, where ‘letters’ on opposite strands recognize each other, and where Cs bind to Gs.”
Now, as one might imagine, all sorts of questions started popping into my mind, and these questions, I suspect, were what popped into the minds of all the people sending me versions of this article. Notably, in no version that I saw, were we given much of an explanation why scientists were looking for the structure in the first place. The first article merely notes that the structure has been known about for a while, but has only now been witnessed operating in vitro. What I'd like to know is, when was it first noticed or suspected, and why? It strikes me - with apol0gies to professional scientists - that there's a problem here, and it may just be my stupidity and lack of understanding, but in any case I'll crawl way out on to the end of the twig and speculate anyway. If this newly discovered four-stranded knotty structure is natural and integral to genetic processes, and since its bonding rules are different than those of the double helix, it would therefore seem to imply a nasty question: why would it have gone unnoticed? Did it interfere with the discovery and development of the double-helix structure? Wouldn't such a natural structure possibly inhibit or at least cause some confusion in the discovery of the helix?
Or to put my intuitions "country simple": something appears not to add up here(and, as cautioned, it may be due to my invincible ignorance and stupidity).
Scientists have noted that this is a structure that appears to be some sort of regulatory structure, appearing and then disappearing under certain conditions. If this is the case, then my question might answer itself, for a temporary structure might not inhibit the discovery of the helix.
But there's another possibility that struck me as I was reading this article, and this possibility will, I suspect, put the stamp of proven and irrefutable invincible stupidity on me: what if this structure is, somehow, not natural? What if it has arisen recently in response to certain factors? It's that "C binding to C" thing that flummoxes me, for it's as if we're being told that there is a new - albeit "temporary" - base pair, and the "pair" in this case consists of the same thing! In other words, what if we're looking at one of those "major mutations" that - like the Grand Unification in physics - is the holy grail of evolutionary theory? And once we've admitted that possibility, then one faces another: if it arose recently, was it injected? (And for that matter, might it be possible to view the strange four-stranded regulatory "knot" as a kind of epigenetic code?) And the ultimate question: is this natural, or artificial?
I don't know, of course, the answers to any of these questions, and in asking them I'm sure I'm provoking guffaws of laughter in certain professional circles. Nonetheless, that said, I still cannot help but feel we're not being given the whole story here, and that there are some prickly questions which cannot be so easily smoothed over.
See you on the flip side...