Thursday, November 15, 2018

Failure: The Real Secret Sauce of Engineering

I took one swing at Vijay Pande's overly rosy piece on applying engineering methods to biology and medicine and similar minded efforts were published by Ash Jogalekar at Curious Wavefunction and Derek Lowe at In The Pipeline. Perhaps I shouldn't make another go, but it is a new excuse to explore an old fascination of mine.  Pande's subhead was "Billion-dollar bridges rarely fail -- whereas billion-dollar drug failures are routine".  I can't argue that.  Actually, it would seem from an informal search that billion dollar bridges are actually much rarer than billion dollar drug development programs.  Obviously they exist -- I've traversed the new Tappan Zee Bridge which came in over $3B.  On the other hand, a second crossing at perhaps the most notorious spot in bridge engineering history, the Tacoma Narrows, was built earlier in this century for only $0.8B.  What I wish to explore are the failures of bridges and other structures of any cost, as it is the analysis of failures that frequently propels engineering forwards.  That analysis is enabled by the relative simplicity of human engineering and the artifacts it uses and creates.  Conversely, analyzing the failure of new drugs is nothing like that.

Thursday, November 08, 2018

No, the Groves Fallacy Can't be Retired Yet

Vijay Pande has a thought-provoking piece in Scientific American on the Groves Fallacy, though in the end I'm afraid mostly what he provokes in me is the thought that he's in most cases pretty far off base. Titled "How to Engineer Biology", he claims that the Grove Fallacy -- the idea that biology can't be tamed by engineering -- is quickly being put to rest.  And Pande isn't some naive Silicon Valley type, but a professor at Stanford whose lab works in experimental biology.  So he has some street cred -- but that doesn't mean he isn't mostly wrong.

Monday, November 05, 2018

Illumina Buys PacBio: More Thoughts

Illumina surprised pretty much everyone in the genomics community by announcing the purchase of Pacific Biosciences.  I had spent Thursday deep in the weeds of a combined PacBio-ONT-Illumina dataset, so was caught completely by surprise on my commute home by an email asking for my comment.  If you do want to hear hot takes on it from myself and AllSeq's Shawn Baker, Theral Timpson over at Mendelspod interviewed us that night.  There has of course been much discussion of the deal and tributes.   I've had the weekend to ponder things, and here are some somewhat better thought out and detailed comments -- though I don't believe I've retreated from any of the themes in the podcast.  I've grouped the thoughts into a few themes.

Tuesday, October 16, 2018

You Can Be Impatient Running MInIONs, But Not Feeding Them

Yes, it's been way too long since I wrote here.  Even longer since I did so with any regularity.  There was always some list of things draining my time and energy.  But I resolved this week to get back on the horse -- and that was even before today's bit of dilithium news. In particular, in one twenty-four hour span three different people remarked on the prolonged hiatus -- a professional contact, a commenter on the blog and finally some very cutting remarks from Draco (aka TNG).  And what better way to get going again but to kvetch about Oxford Nanopore's supply chain model?

Tuesday, July 31, 2018

Two Museums Guaranteed to Fluor You

I've been horribly neglecting this space for an extended period.  Contributors to that include a TNG eclosing from high school, ferrying grandparents, a milestone (or is it millstone?) birthday and a 10 day vacation with poor Internet service.  Oh yeah, another one of those starts Thursday.  Then there's keeping the genome factory going -- at times I feel like a worker in Fritz Lang's Metropolis.  But someone even noticed and emailed me today whether this hiatus would end, which is beyond reason enough to get going.  But tonight's entry has nothing really to do with biology or genomics, but rather hearkens back to the first science I fell for.

Monday, June 18, 2018

LC2018: VolTRAX

In my preview ahead of London Calling, I suggested that VolTRAX is a device that still hasn't found its raison d'etre.  With the meeting, the device officially pre-launched and the company is now taking pre-orders for delivery in the Fall.  And it still feels like a device which hasn't yet found its purpose, though Clive Brown presented a dazzling (if perhaps distant) vision of where VolTRAX might go.

Wednesday, June 13, 2018

LC2018: Flongle, Ubik-a-something and Metricoin

London Calling has been over for nearly three weeks.  I originally wanted to write up at least something after the first night, but fatigue overcame me and I didn't get anything useful put together.  And then travel and more fatigue set in.  But beyond that and the usual temptation to procrastinate, there is the challenge of forming a coherent narrative from all the different threads at the meeting.  There's all the Oxford Nanopore official announcements and then various user presentation tidbits.  After several failed mental attempts to compose a big picture take on everything, I've decided to try to write a series (number yet indeterminate) of posts that will focus of various axes of the meeting.  Hopefully they won't be to redundant -- or self-contradictory -- and that by following one particular thread I can actually condense some coherent thoughts.  This first such thread starts with Flongle.