Polling junk DNA

I missed this poll by Chris Gunter yesterday, asking “If you are a non-genomicist, can you tell us if you thought/were taught much of the genome was “junk”?

Well, I’m 1) a day late and 2) not a non-genomicist, but I’ll reply anyway, because we need a little history review.

In my Eukaryotic Genomes course in grad school (in the year the draft Human Genome sequence came out), I was taught by Tom Eickbush, not so much about ‘junk DNA’, but about ‘selfish DNA’. The point is largely the same regardless of what we call it. Among the first papers we read in Eickbush’s class were the classic Doolittle and Sapienza and Orgel and Crick papers on selfish DNA.

The key argument of these papers was this: parasitic DNA that can replicate itself within the genome requires no other explanation for its existence other than is ability to replicate, period. It does not need to be functional, from the perspective of the organism. It may acquire a useful function. But in general, absent evidence of such a useful function, we don’t need to ask the question, ‘what is the function of this DNA?’ There’s no mystery why it’s there – because it can replicate. Continue reading “Polling junk DNA”

ENCODE Media FAIL (or, Where’s the Null Hypothesis?)

I’m ready to drink myself into a stupor, and not because it’s my birthday. This week we’re seeing a massive science reporting fail on a large scale. And just to be clear, I’m not only (or even mostly) blaming reporters.

We’ve known for a long time that protein-coding genes are regulated by non-coding DNA sequences, ‘gene switches’, if you will. We’ve known for decades that the genome contains many ‘gene switches’. (See the references in this review.) That’s uncontested.

ENCODE is significant because they’ve provided a very useful data set, and not because they’ve a) shown that non-coding DNA is important (we knew that), or b) most of the genome has phenotypically important regulatory function (it does not), or c) that most of the genome is evolutionarily conserved (not true either). What they have shown is that much of the genome is covered by introns, and it is hard to find biochemically inert DNA, which those of us who’ve tried to generate random, ‘neutral’ DNA sequences (for say, spacers in synthetic promoter experiments) will agree with.

Now, let’s see how major media stories are handling the significance of ENCODE (h/t to Ryan Gregory for compiling the list of stories): Continue reading “ENCODE Media FAIL (or, Where’s the Null Hypothesis?)”

Linkonomicon V



from Nerdist

Happy Birthday, Mike!

Please join me in wishing Mike – co-founder of The Finch & Pea, my former co-indentured servant of Barak Cohen’s lab, nice guy, sci-fi guru, and irritatingly talented piano player – a very happy birthday. Remember, buddy, its not how old you are, it’s how old you feel – we are going to need a lot of candles.

. . .AND MANY MOOOOOOORRRRREEEEE!!!

Congratulations Kerri!

 

You know that moment when your friend does something so amazing you can’t help bragging on them? Try not one, but two, in one week. Below you’ll find video of my friend Kerri Morgan winning the bronze medal in both the 100m & 200m Women’s T52 sprints at the 2012 Paralympic Games.

Go to minute 56:50 for the Women’s 200m T52 final.