An ode to junk

It is an unfortunate circumstance that ENCODE publicity decided to declare “junk DNA” dead, again. It’s not a totally unique position. Creationists and John Mattick have argued that there is no useless DNA for ages.

The demise of “junk DNA” is a fait accompli of the way “functional” is defined. It is not a definition of “functional” most of us would recognize. Ewan Birney, who should know, explains that when ENCODE says “functional” they mean “not biochemically inert in at least one of our many assays*”. As Mike has noted from his own research experience, many totally random DNA sequences synthesized in a tube are “not biochemically inert” nor are they biologically “functional”.

The fact is, if you only think of “junk DNA” as a problem, you aren’t seeing the forest for the trees – and you certainly are lacking a touch of poetry in your bleak soul. Continue reading “An ode to junk”

Sometimes you wanna go…

…where everybody knows their genomics. Bum bum bum.

Which is as far as I’m taking that, because I have the bad feeling that y’all would suggest that I’m the Cliff Clavin around here (I’m so the Carla).

Technology willing (let’s all take a long, suggestive look at Mike for a moment), we will be doing a live Google Hangout to talk about the ENCODE project tonight (Tuesday, 11 September) at 9PM Eastern. We’ll chat about what it means for science, “junk DNA”, and who (if anyone) actually knows what they are talking about.

Oh yeah, it is BYOB until we get that whole virtual liquor license thing sorted out.

*Leave a comment here or tweet @joshwitten or @finchandpea if you are interested and need a hangout invite.

The genome is a huge haystack. How do you find the needle?

The complexity of the machinery by which our cells run is so extreme that one of the key questions in biological research is, why doesn’t the whole thing just collapse like a house of cards in a tornado? Another way of phrasing this question is to ask, where does the information come from to keep everything running smoothly?

Consider this: the crucial task of gene regulation is carried out in large part by transcription factors, regulatory proteins that recognize and bind to very short, degenerate DNA sequences located somewhere in the rough (sometimes very rough) vicinity of genes. Once they bind, transcription factors recruit the machinery that activates their target genes. (You can also have transcription factors that repress target genes.) This is all good, until you consider the fact that a human transcription factor has to find its target sequences from among the 3 billion base pairs in the human genome. Some plant and fish transcription factors have to search through genomes with more than 100 billions base pairs. So the question is, why don’t transcription factors get lost? Where are they asking for directions?

On finding needles in the genomic haystack Continue reading “The genome is a huge haystack. How do you find the needle?”

Genomycism: “Deflating the Genomic Bubble”

Genomycism – the unsubstantiated belief that the cataloging of the genomic sequence of an individual conveys useful understanding about their ancestry, current characteristics, and disease risk with high degrees of accuracy and predictive power.

An important policy forum article has appeared in the most recent issue of Science discussing the expectations for the benefits of genomics, the issues created when those expectations are unrealistic, overinflated, and over-hyped[1]. Continue reading “Genomycism: “Deflating the Genomic Bubble””

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