Friday, December 09, 2016

Siddhartha Mukherjee's The Gene, An Intimate History & the Crafting of Scientific Stories

Back in 2011,  I read and reviewed Dr. Siddhartha Mukherjee's book on the history of cancer therapy, The Emperor of All Maladies.  I liked the book, but as is my character I also listed some criticisms.  It was a very pleasant surprise to one day discover an email from Dr. Mukherjee engaging me on my points.  A real author, writing me!  Fast forward to this fall, and I had some inexplicable inertia to reading his new book, The Gene, An Intimate History.  This time he drove the process forward, asking if I'd like to read and review the book and if so could his publisher send me a copy?  Wow!  Having just finished the book, here goes the full review.

Tuesday, December 06, 2016

Reversible Terminators: Not Just For Sequencing

Reversible terminator nucleotides lie at the heart of sequencing-by-synthesis systems such as Illumina.  These nucleotides in their original state cannot be extended, terminating DNA polymerization.  But with the correct chemical treatment, the block is removed and polymerization can continue.  A recent paper moves the concept from sequencing to making large single mutation libraries.  The authors have apparently also applied for a patent (according to the Conflicts of Interest statement accompanying the paper), though that does not turn up on Google.

Friday, December 02, 2016

Oxford Nanopore New York City Meeting, Day 2

The second and final day of Oxford Nanopore's New York User Meeting ran today.  I've again been mining tweets, since I wasn't on site.  Oxford itself has posted a summary of Day 1, which has the enormous benefit of the author being present! I'll make a few quick summaries.  The tweets for today can be found in two semi-thematic Storify entries: one gives general coverage and of ONT's demos, whereas the other covers ONT's technical talks and talks by users.

Thursday, December 01, 2016

Oxford Nanopore New York City Meeting, Day 1

Oxford Nanopore officially kicked off its Community Meeting in New York City today; a training session took place yesterday.  Already there have been several interesting announcements and presentations, including a new prototype sample prep gadget, a new basecaller which improves homopolymer calling, a read-both-strands approach that isn't 2D sequencing and details on multiple human genomes run on MinION. A reminder: I'm working only from tweets; I'm not at the meeting.

Wednesday, November 30, 2016

Is PromethION a Strategic Error?

Be prepared for another burst of Oxford Nanopore coverage; their annual Community Meeting in New York City begins on Thursday (perhaps while you are reading this).  I won't be attending; only so many absences from the day job are ultimately feasible each year, and I've long since hit the limit.  Hopefully some prolific tweeters will keep everyone updated, and I can summarize from there.

As with most posts on Oxford Nanopore, my piece on the closure of the Illumina litigation captured some comments; I think it is reasonable to expect more on the piece on the opening of litigation by Pacific Biosciences.  How you perceive the ambiguity around whether they were using an MspA pore in the R6 and R7 chemistries or not tends close to a Rorschach test.  But with that behind us, attention can focus on their current state and progress. Now, I'm going to project some critical ideas around one of their platform pieces, but I have no delusions that they will affect Oxford's course.  It wouldn't shock me if Clive had a tart seven letter response, the only question being if the last three letters form a pronoun or a preposition. I don't have any inside information nor do I have any direct financial interest in the company, in case you are wondering.  As my title suggests, what I'm going to argue is the case that pursuing the launch of the PromethION instrument is an unnecessarily risky detour.

Tuesday, November 29, 2016

Revisiting Mendel

In yesterday's post, I flagged a small factual error in Siddhartha Mukerherjee's The Gene.  I really liked Mukherjee's prior history of cancer, The Emperor of All Maladies, and was thrilled when Dr. Mukherjee wrote a thoughtful response to the criticisms I did make.  So it was another happy moment recently when he asked me if I'd like a copy of the book so I could review it.  I'm only about a third through the book, but it is definitely worth reading (why did I wait so long? no good reason).  Since I like it, when I get to a full review I'll probably be mostly in "this is what I would have suggested if I were an editor" mode.  I'm not ready for that yet (finishing the book is a pre-requisite!), though cryptic notes are piling up in my Evernote on the topic.  However, there is a specific part of history covered in The Gene which warrants separate treatment, using the book more as a springboard than as the central subject.  That concerns the amazing man widely regarded as the founder of the science of genetics, Gregor Mendel.

Monday, November 28, 2016

Nostalgic for Fly's Eyes

Kumar Thangdu's mission of prodding me has contributed to a bout of nostalgia for one of my graduate student rotation projects.  He asked in a tweet how I'd allocate funds if I was given stewardship of a billions in grant money.  If you want to get some big results but are willing to be very patient, then a great way way to invest is in model organisms.  As a rotation student at Harvard, I spent several months pushing Drosophila melanogaster, the not-so-humble fruit fly.