Featured Topic 9/12: DNA and dinosaurs

As has happened before, this month has involved important new papers related to both paleontology and genetics.  It's probably an overstatement to assume that the new papers published in either of these fields will have the same impact as those published in the last week of February 1969, but they are important enough that it's best for this month's featured topic to cover both of them. With that in mind, this month's featured topic is split into two parts: the first portion is written by me, and the second portion is written by EWilloughby.

Junk DNA: is it really junk?

This month the scientific world has been abuzz with the news of ENCODE, a genetics project which has documented the function of a large portion of our non-coding DNA. The way this project is described by most the news stories about it, including the New York Times and the linked article in Science, is that until recently it was assumed that only a small portion of the human genome did anything all, and ENCODE has completely reversed that view.

But has it really? ENCODE's research is certainly a major step towards understanding the function of the human genome, but the idea that most non-coding DNA still has some function has been known for over a decade. As is pointed out here, this is another situation where the popular media is giving an inaccurate impression of new research in order to "dumb it down" for a popular audience. In some cases, although the DNA does indeed have a function, it also is only a minimal function that could have been accomplished by a far smaller quantity of DNA.

Here's an analogy which might make this clearer. In 2008, when I moved into the house where I currently live, a cheaply-made dresser I had purchased in my previous house did not survive the move. At some point on the moving truck, most of the panels of plywood became detached from one another, and by the time it arrived it was no longer possible to open any of the drawers. At first I considered just throwing the broken dresser away, but eventually I decided that I might as well keep it around. The reason I did was because keeping it in my house doesn't do any harm, and parts of the broken panels and drawers are still sometimes useful for things like propping up legs of wobbly tables and chairs.

Does that mean the dresser has a function? It technically does, because parts of it are still being used for something, but it certainly doesn't function as a dresser anymore.  The function it's currently performing could be accomplished by something far simpler than a dresser, and the only reason the dresser still exists is because using bits of it to prop up tables and chairs is more convenient than getting rid of it entirely. This is the sort of function that exists for a large portion of our non-coding DNA.

I've posted before here and here about how the popular media often tends to distort new scientific discoveries, and this is yet another example. This time, however, the cloud may have a silver lining. Because of how important ENCODE's research is, and how few news sources have described it accurately, the media's description of this research has been receiving a larger-than-usual amount of criticism from scientists. Perhaps in the long term, this will make scientists more aware of the general problem of the media distorting scientific research, and encourage them to make more of an effort to prevent it.

Maybe Mei long really is always sleeping

When I first told Nobody that a new specimen of Mei long had been unearthed and described, his first reaction was to joke, "This one wasn't in a sleeping pose as well, was it?" Of course, that's exactly what the new specimen of Mei is doing after all, as the recent PLoSONE release shows. The authors describe the new specimen as having adopted a posture "nearly identical to the avian sleeping posture of the type specimen". Seriously, what are the odds? Did Mei really just sleep all the time? Was it an extraordinary coincidence? Did the tiny troodontid hibernate?

The new specimen answers none of these questions with certainty, though it answers a few others. The phylogenetic position of the new Mei specimen resolves the same as the holotype, as a basal troodontid (the new specimen resolves Mei as most closely-related to Byronosaurus and Talos as well). The new specimen is also likely to be an older juvenile or small adult, while the holotype was a young juvenile, so we now have a better sense of the animal's growth stages. It has a curious amalgamation of both juvenile and mature adult skeletal features, which leads the authors to speculate that Mei might be a pedomorphically small troodontid with typically "juvenile" traits retained into adulthood. Pedomorphism, or neotony, is the same phenomenon that we see in domestic dogs that gives some breeds very small size and floppy ears - traits typical of puppies in wild canines - among other traits.

Of course, what seems to be of interest to most people about this new specimen is its sleeping pose. The posture of the new specimen is almost a perfect mirror image of the holotype, having its neck arching to the left rather than to the right, as in the holotype. The authors note that the Mei specimen lacks the typical "opisthotonic" or pugilistic features that are common in death from volcanic ash, as the animal reacts to the pain and stress of dying from asphyxiation and extreme heat. They give three possibilities for why this would be the case: the animal may have been buried in ash faster than its body could have responded, it could have died in a manner that didn't stimulate the typical perimortem posture, or that troodontids simply lacked such a response (which they consider unlikely). They suggest that one possible explanation is that the animal took shelter in a burrow shortly before dying, and as such avoided the intense heat and so on. The authors also speculate that the Mei may have died in the posture to shield itself from the falling volcanic ash that took its life. They do not explore a third possibility, which is that the tiny troodontid was such a voracious partier in its narrow waking hours that it simply needed to sleep almost all the time to work off all that sex, drugs and rock and roll.