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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 Agahnim 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.
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:iconsekele:
Sekele Featured By Owner Oct 1, 2012
honestly, since when do the media listen to reason to begin with?
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:iconsinande:
Sinande Featured By Owner Oct 1, 2012
OK, I wasn't interested enough in ENCODE to do more than acknowledge its existence. Now I feel like I have to look more closely at what they mean by "function". Having read the news article in Science, I'm a bit dubious.

I'm not at all sure that things like binding TFs, being transcribed or being conserved are good indicators of function. TF binding doesn't have to mean gene expression, transcripts might be transcriptional noise destined for destruction, and a stretch of DNA can be crucially important and even have highly conserved functions while displaying a huge amount of variation (MHC genes with their hundreds of alleles, eve stripe 2 enhancer...).

(Also, did I read that right? Were most of the cell types they studied in more detail fucking *cancer cells*? :o)

I just... dunno. I hope there's actually more to it than it seemed from that article, or if there isn't, that the ENCODE people and those who'll use their data understand exactly what they have and haven't found.
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:icondoctormo:
doctormo Featured By Owner Sep 30, 2012  Professional Digital Artist
Wasn't there a piece on the SGU about science reporting? Something about how original authors or extracts having the greatest impact on miscommunication and incorrect reporting once it's gets to the popular press.

The conclusion was that scientists should take greater care and put more energy into explaining things. Dumbing things down isn't a problem if it's "lies to children", almost right, along the right path as right, but lacking in nuance.
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:iconriotgirlckb:
riotgirlckb Featured By Owner Sep 30, 2012  Student Traditional Artist
The media definitely dumbs things down for the audience, as :iconomega-werewolf: states above people are lazy and sometimes dumb, the writers may be too lazy to write an extended article but may also cut it back and dumb it down to keep the attention of the target audience, even the most attentive of people are going to start skipping sections if the article is too long.

and I like the idea of Mei Long being a party goer haha thats great :D
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:iconikechi1:
Ikechi1 Featured By Owner Sep 30, 2012  Hobbyist General Artist
also how much do you think the media is going to distort the information on baryon particles around the milky way
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:iconikechi1:
Ikechi1 Featured By Owner Sep 30, 2012  Hobbyist General Artist
the sleeping dragon continues to snooze
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:iconebolasparklebear:
EbolaSparkleBear Featured By Owner Sep 30, 2012
I think the media dumbs things down for a few reasons:

The media is lazy and everything needs to fit into a soundbyte.
The target audience is dumb.
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:icondeanreevesii:
deanreevesii Featured By Owner Oct 1, 2012  Professional Traditional Artist
I think much of the time the target audience is dumb because they aren't challenged by the media though. Like the web-news. Yahoo has about 33% Entertainment, 33% sports, and 33% actual news. People read the gossip because it's there and easily accessed, but I imagine that they'd read more relevant news if it was dominant on the "news" sites.

But hell, maybe not. Maybe I'm just wishful thinking ;)
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:iconebolasparklebear:
EbolaSparkleBear Featured By Owner Oct 2, 2012
I think you're being too wishful, at least in Ammurkah! :P
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