Tag Archives: dna

Jargon will make time travel very confusing

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This was a gift from my sister and is a solid science fictiony quote – one that I’m quite happy to put on my wall1.

The Time Machine by HG Wells (1991 Bantam Classic Reissue from library of Josh Witten)

The Time Machine by HG Wells (1991 Bantam Classic Reissue from library of Josh Witten)

Being a fan of, but hardly an expert on HG Wells2 and being a fan of, but hardly an expert on the history of science, I had to wonder if this quote was actually from HG Wells’ The Time Machine, or was from one of the movie adaptations. As you will see, this is an easy question to answer. The trick is figuring out why you might want to ask the question in the first place.

HG Wells was brilliant and reasonably familiar with scientific research. To pen that line, he would also need to be a time traveler himself. Continue reading

The Eagle Pub and the BRCA2 cycle path

Despite its tiny size, Cambridge (UK) is full of science travel destinations. One of my personal favourites is The Eagle. This pub is the location where, in 1953, James Watson and Francis Crick first announced the helical structure of DNA. Their lab was right across the street, and when they solved the puzzle (after perusing Rosalind Franklin’s famous image) they went to the pub to tell everyone. Francis Crick announced that they’d “discovered the secret of life”.

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Two months later, they published the work in Nature, but the news was first announced right in this pub. Now, 50 years later, the helical structure of DNA has become iconic. You see it anywhere from scifi movies to biotech company logos.

IMG_0355Cambridge is particularly proud of its helix, and has even placed a statue of a DNA helix along a cycle path just outside of Addenbrookes hospital. If you’re on the right side of the train traveling from London to Cambridge, you can see it if you know where to look.

That helix structure marks the start of the BRCA2 cycle path: the cycle path along the train track is painted in stripes of four colours, according to the genetic sequence of BRCA2 – the gene which, when mutated, causes significantly increased risk of breast cancer. I wrote more about the cycle path here.

In a town that can’t get enough of DNA, it’s tempting to go along with the  biochemical geekery, and so after the 2011 SciBarCamb unconference a few of us posed in front of The Eagle pub with a model of two basepairs of DNA made out of balloons. Just another day celebrating DNA in Cambridge.

eagleDNA(Balloon DNA photo by Jim Caryl. Other photos by me.)

And don’t forget to check out our Have Science Will Travel map:

Held: Genes are products of nature

Today the US Supreme Court rules that there cannot be patents on genomic DNA information (PDF – 139kb), only modified DNA products like cDNA. Note that the decision was effectively unanimous, the opinion was written by Thomas, and Scalia’s concurrent opinion is essentially an admission of ignorance in the specialty field. I have not had time to read the full opinion, but at initial review this seems like a very reasonable result. Naturally occurring DNA sequences are, well, natural. Sequences modified with intent may be patent eligible. It will be interesting to see in the future if discovery of naturally occurring sequences that are identical to patented sequences modified naively to match a natural variant will invalidate patents.

Myriad’s DNA claim falls within the law of nature exception.Myriad’s principal contribution was uncovering the precise location and genetic sequence of the BRCA1 and BRCA2 genes…Myriad did not create or alter either the genetic information encoded in the BCRA1 and BCRA2 genes or the genetic structure of the DNA. It found an important and useful gene, but groundbreaking, innovative, or even brilliant discovery does not by itself satisfy the §101 inquiry…Myriad’s patent descriptions highlight the problem with its claims: They detail the extensive process of discovery, but extensive effort alone is insufficient to satisfy §101’s demands. Myriad’s claims are not saved by the fact that isolating DNA from the human genome severs the chemical bonds that bind gene molecules together. – SCOTUS (PDF -139kb)

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.

Breaking in Order to Build

Image courtesy of the Journal of Cell Biology

Image of labeled (red) DNA breaks in a single cell courtesy of the Journal of Cell Biology

Do you ever think about how every time you encounter something new your brain adjusts and rewires and makes molecular changes so you can remember this new object in the context of what you already know? I know I do, though that may be a by-product of my neuroscience upbringing. Even if you don’t think about it, it’s happening. Complex changes in the numbers and amounts of gene expression are critical to developing and maintaining memories. And as it turns out, breaking the DNA in your brain cells into pieces is also part of the process.

Continue reading