Directed Panspermia Doesn't Belong In Schools (and Probably Never Will)

Opening to the Ideas section of the Boston Globe this past Sunday, I was immediately faced with a grotesque site.  Nothing to do with the appalling terrorism of fifteen years ago, but instead the Globe putting front-and-center in the section a truly awful idea, which the subhead trumpeted "Creationism can have a basis in science - if aliens are involved".

Portrait Of A Genomics Instrumentation Impresario

Veteran biotech reporter Luke Timmerman's new book, Hood: A Trailblazer of the Genomics Age, is a valuable exploration of one of the leading figures in the early development of genomics and proteomics.  This in depth look at a key scientist covers not only his achievements and glories, but also his less than stellar moments and tendencies. Timmerman has combined his own interviews and research with nuggets pulled from prior news articles and oral histories of scientists who crossed paths (and sometimes figurative swords) with Hood.  While the book has issues, I would recommend it to anyone interested in the history of biotechnology.  For the full review, including numerous spoilers, read on.

Four Things You Might Be Surprised Can't Be Done On An iPhone or iPad

In well under a year, I've been sucked into Apple's mobile ecosystem.  Partly this was due to lobbying from TNG (he fervently denies receiving any commissions, but I'm still suspicious).  Partly it was due to the Android world not really locking me in; there were just too many things that weren't quite right.  First, the family caught me ogling an iPad Pro and talked me into getting one.  Once I had that, there was confusion over which text channel messages had been sent and getting an iPhone to consolidate them (since iMessage would go to both devices) started making sense.  Plus my Samsung phone was chewing through batteries; that is one area where Apple seems to have a huge lead.  Also the problem of periodically forgetting which device I was on and using a gesture from the wrong operating system.

Wikipedia, and other non-evil things

Tommorrow, TNG will head off for his penultimate first day of grade school.  And unfortunately, that almost certainly means another attempt to indoctrinate him in a catechism I find both depressing and infuriating.  It goes something like this: "Wikipedia is not a reliable source. Wikipedia is not citable. Don't use Wikipedia".

Where the bleep did my pores go??

Another afternoon spent this week in the lab, and another awful MinION run.  I figured that the last run was eminently beatable, given that I ended up with exactly one read aligning to my reference (though perversely, re-calling the data via Metrichor ended up with two reads in the pass folder -- one of which had zero bases in it -- I guess it is a passing null read).  But no, despite coming close to being botch-free on the routine lab stuff, dark clouds came early and the experiment yielded not a single usable read.

Sometimes It's More About the (1D) Journey

I will confess that I had a post planned in advance of which this post is but a faint echo. A grand scheme was going to yield a triumph worthy of brass bands.  But instead, it's barely kazoo territory, but sometimes even a small victory must be celebrated, if only in moderation.

Math Toys, Much Enjoyed!

Last week, I attended a free public talk at the Society for Industrial and Applied Mathematics (SIAM) here in Boston.  This is a wonderful public outreach concept which too few conferences sport.  The speaker, Tadashi Tokieda of University of Cambridge, illustrated a number of fascinating phenomena which can be demonstrated with simple toys or household objects.  Tokieda didn't lecture from a bunch of slides; most of the talk was in the form of live demonstrations -- and demonstrations made with overt glee!  There's a Storify of the entire meeting, in which mine and others of the Tokieda talk can be found.

Infinity's Sad RUD

Almost five years ago, I wrote of voluntarily leaving Infinity Pharmaceuticals.  Particularly due to the novelty (for me) of the voluntary part, at times I've wondered how long I would have stayed there.  Indeed, the offspring asked just that question just over a week ago. I do know now when I couldn't have stayed any longer, as to my great dismay Infinity announced last week it was discontinuing its Discovery operations due to a disappointing drug trial result.

Writing Big

For the past few decades, since the early stirrings that led to the Human Genome Project, technology for reading DNA has gotten immense investment and attention.  Particularly noted, perhaps ad naseum, is the rapid decline in sequencing costs which outpaces Moore's Law for microprocessors.  The converse activity of writing DNA has generally played second fiddle, but these past few weeks have seen a flurry of headlines on that topic.

London Calling 2016: Further Thoughts

London Calling was two weeks ago, and I still haven't written anything beyond the write-up of Clive Brown's talk (note that many of the talks are now view-able via Oxford Nanopore's website).  I did finally make some headway on Storifying the tweets.  After several self-inflicted wounds (starting with failing to read my write-up of the previous experience of trying to post to Storify from the command line, but also from failing to record the details of that final critical command), I did succeed.  This time I decided to group the tweets into several broad categories -- with tweets potentially showing up in multiple categories, though these are a bit rough-and-ready and probably most folks will want to check multiple or all of the stories.  One major value I derive from this exercise is having them to refer back to, so I'll probably feel the pain of erratic characterization the most (though I also have the tweet database, so I could reslice these in new ways).  Anyway, the categories are: de novo Assembly, Bioinformatics and R9, Real Time and Read-Until, PromethION, Microbiomes, Clinical/Human (except Infectious Diseases), Infectious Disease and Biowarfare, Field Uses plus finally Library and Sample Prep (another one that failed initial upload; includes Zumbador and VolTRAX tweets).

There's supposed to be a final one encompassing everything that was left over, particularly general tweets about the conference.  Unfortunately, Storify balked at that one -- have to look again and perhaps break the set into at least two pieces.  (nope: worked with one)

London Calling: Notes on Brownian Commotion

I'm behind on writing up London Calling.  I can partly blame a failing computer -- though rebooting it seems to have righted it for the moment.  A bigger challenge is that I had the luxury of staying in London thru the weekend, and have been trying to pack as much in of England as I can.  To really do justice to everything, I need to scan all the tweets  -- and that will take some time.

But I have dug into everything around Clive Brown's talk (kudos to NextGenSeek for Storifying that portion of the meeting's tweets!_ about the current and future state of the Oxford Nanopore platform, so I will focus on that, with a few side-trips on closely related topics. A few gaps on topics I previewed but didn't show up in the presentation were filled in with chats with Clive.  Plus, the indescribably huge advantage of actually going to a conference are the tidbits gleaned from late night chats over drinks (and no, I didn't ply anyone to get them to spill -- all was coughed up out of pure free will).  I'm going to roughly divide these by the announced timeframe: now, imminently, later this year, perhaps next year and unspecified.

London Calling Preview

ON Thursday and Friday this week Oxford Nanopore will be holding their second annual London Calling meeting.  I successfully defended my schedule this year, so I'll be on the ground there. If you follow me on Twitter and don't want to be buried in nanopore tweets, mute the hashtag #nanoporeconf (a rather large hashtag for talking about nano stuff!)  LC is OxNano's premier event, so what might we see from the company?

Inconstant lines

If you order chemicals, then the supplier provides a certificate of analysis, which shows the amounts of impurities or their limit of detection.  Fir physics experiments, one can purchase components which have been carefully cast or machined to precise dimensions. Barring errors by the manufacturers, these reagents and components can be relied upon, as their consistency is known.  Alas, for biological systems, such constancy is often a mirage.

Sickle Cell Anemia: An underprioritized disease?

The Sunday Boston Globe today had a front page piece by STAT's Sharon Begley that asks some challenging questions about prioritization of disease research.  Poking around the STAT site, I found that the original article was even longer and better, but between the important issues it raises, some interesting peripheral stuff and at least one gaping hole, there's plenty to discuss.

Kendall Square Tech/Biotech/Biopharma Needs to Get Vocal About Transit!

Earlier this week, the current big Boston-area mass construction transit project, known as GLX, went through a near-death experience.  The project, having been mismanaged to be over budget and behind schedule in the early going, was approved to survive in a stripped down form.  Numerous political types were quoted supporting the project, albeit complaining about contributions their towns were making to keep the project alive. What wasn't heard was any sort of support from the tech, biotech and biopharma companies which crowd Kendall Square.

Exploring Critiques of Siddhartha Mukerjee's The Gene, An Intimate History

My finely tuned skills in the art of procrastination KOed my plans to see Siddhartha Mukerjee's talk tonight at a local bookstore (apparently with Henry Louis Gates) to promote Mukerjee's new book The Gene: An Intimate History -- the event sold out.  Perhaps I could have found a scalper, but I decided I'd just head home.  Mukerjee's first book, the cancer history The Emperor of All Maladies, was very well received (even spawning a PBS series), and I was impressed that Mukerjee took the time to contact me after I wrote a review in this space.  The new book has been taking quite a bit of criticism, and even more so his New Yorker piece that preceded it (and I assume is derived from a portion of the book).

Around the World in Amino Acids

This post is pure whimsy, growing out of killing time on a train ride. The not-so-serious question: what is the geography of amino acids?  If I search for them by name in Google Maps, what will I find?  With just Google Maps, plus some Google Translate thrown in, I found a few surprises.

Genia Publishes Platform Progress

Nanopore sequencing developer Genia published in PNAS last week a study demonstrating the basics of their current approach to sequencing.  I say current, because Genia has gone through a number of iterations and on at least two occasions promised to be going into beta in a 6-9 month timeframe.   The paper demonstrates the basic concepts of a sequencing system and generates some short reads, but also suggests that Genia won't be hitting beta sites in the near future either.

Protein Homeostasis: Has it Hit The Classrooms Yet?

I wrote a piece earlier this year suggesting that introductory Biology textbooks should emphasize protein complexes more.  My basis for assuming that they generally don't isn't very good: a single textbook in use in TNG's high school class, which sports a copyright date from a decade ago. I also remember what I was taught in high school and college courses, which I would rate as not bad and truly excellent (respectively), plus I was a teaching fellow for one semester of intro bio at Harvard.  I now have another suggestion to cram into every biology course: an overview of ubiquitin-proteasome system.

Mosquito Genomes: Chance for Long-Range Companies to Shine

Friday's New York Times carried a front-page illustration of the current status of the Aedes aegyptii genome, accompanying an Amy Harmon story on efforts to improve the currently highly fragmented state of this genome

Hey @DrKatHolt @rrwick, there's a Bandage plot on the front page of the @nytimes today! #NoFooling @MarkKunitomi pic.twitter.com/a1n6QyQWr3

— Adam Phillippy (@aphillippy) April 1, 2016

The pice has seen a lot of opinion on Twitter with regard to its value and other issues (such as calling an assembly a map -- which to me is correct as the perfect genome sequence is the ultimate physical map!)

This whole thread. My science peeps keep me here. ❤️ https://t.co/96mifMD0da

— a muse (@_a_muse) April 3, 2016