“What is your quest?”

That thing where you indavertantly facilitate a polite-ish discussion between Michael Eisen and Ewan Birney about ENCODE’s claims regarding “biochemical function” in the genome using modified Monty Python and the Holy Grail* quotes:

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With a “wafer thin” side of Open Access:

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You can check out the Storify of the #MontyPythonidae edition of #SCInema here.

*An apropos and overused scientific metaphor itself.

Baby’s First Genome

Human_genomeSomeday in the future each child that is born will have a file of their genome sequence prepared at birth. For some newborns in Boston, Kansas City, San Fransisco, and Chapel Hill the future is now. The National Institutes of Health is funding a new initiative to examine how the early availability of a child’s genome  will affect medical care decisions and the families. $25 million dollars over 5 years is to be allocated between research sites. Each location is approaching the issue of infant genomes slightly differently. Continue reading “Baby’s First Genome”

Breaking in order to Build: Part 2

Image Courtesy of Michael Schmidt
Image Courtesy of Michael Schmidt

I recently wrote about how breaks in neural DNA may be part of the process our neurons use to generate new memories. About the same time, I found a new study in Science that addressed the role of the genome in neurons from a different angle. It turns out that Drosophila (fruit flies) have particularly heterogeneous genomes in the neurons associated with learning and memory. Now let me back up and explain exactly what I mean by heterogeneous genomes and how that can affect learning and memory. Continue reading “Breaking in order to Build: Part 2”

Doolittle disagrees, politely

The rebuttal to the ENCODE project’s claim to have vanquished junk DNA by Graur et al. got a lot of attention for its scathing rhetoric. If you already have enough troubles in your life, W Ford Doolittle penned a cogent, but polite rebuttal of the claim in PNAS.

…what would we expect for the number of functional elements (as ENCODE defines them) in genomes much larger than our own genome? If the number were to stay more or less constant, it would seem sensible to consider the rest of the DNA of larger genomes to be junk or, at least, assign it a different sort of role (structural rather than informational)…A larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon, is needed.

Unfortunately, you need a subscription to read the full length article, which I do not. Therefore, I’m not endorsing all of Doolittle’s arguments, but I do like that he seems to agree with my assertion from “Decoding ENCODE” that evolutionary theory expects junk DNA in species with the population and genomic characteristics of humans.

*Hat tip to Leonid Kruglyak.

So I take it you aren’t happy with ENCODE…

Mike is very busy being an awesome scientist. So, I have the duty of reacting to the latest “ENCODE takedown” published by Graur et al in Genome Biology and Evolution: “On the immortality of television sets: ‘function’ in the human genome according to the evolution-free gospel of ENCODE”. The title kind of tells you that the ENCODE consortium has a snowball’s chance in Hell of coming out of this one looking good – not that the paper was written by unbiased critics. Continue reading “So I take it you aren’t happy with ENCODE…”