Category Archives: Genomics

What does the Hela genome agreement imply for consent and genome data usage?

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All opinions my own and do not necessarily reflect those of Novo Nordisk.

A fair amount of reporting (for example here, here and here) has gone into the recent news that the NIH and the descendants of Henrietta Lacks have reached an agreement about the conditions under which the genome sequence of the HeLa cell line will be shared.  The basic parameters are that researchers wanting access to the data will need to apply for permission, the application committee will include members of the Lacks family, any publications will acknowledge the contribution of the Henrietta Lacks, and future genome sequences will be submitted to dbGAP.

This is a generally welcome development, and in no small part due to the work of Rebecca Skloot.  Her book, The Immortal Life of Henrietta Lacks provided the impetus to the current developments by popularizing the story of Ms. Lacks and the cell line derived from her tissues.  However, this agreement also can be seen as a precedent of sorts, and the future implications for the ethics of consent, genetic information sharing and genomic research are unclear.

Whose genome is it, anyway?

In Pasco Phronesis, David Bruggeman penned a post on some of the possible implications.  He discusses one of the key elements of genetic consent that I generally haven’t seen elaborated on much in the current literature: familial consent and exposure.   To what extent do those who share part of a sequenced genome have a say in the granting and rescinding of consent for the usage of genetic information?   Continue reading →

Major League Baseball should be all over the quantified self movement

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All opinions are my own and do not necessarily reflect those of Novo Nordisk

Baseball players break down.  Their performances fluctuate.  As a group there are some interesting generalities with respect to how pitching, hitting and fielding change with age.  But the error bars are huge.  There are many things we still don’t know about baseball players, about why one prospect hits the ground running and another flames out.  And we also don’t know if there is any way to know, since the task of putting together the skills needed to play major league baseball may be one of the most complex of the major sports, and understanding complexity is hard.

But it seems worthwhile to give it a try.

The Mystery of the Missing Ligament

Let’s talk about R.A. Dickey for a minute.  Not because he’s a highly interesting human being, although he is.  And not because he’s a knuckleballer, which is fun and interesting due to rarity and the entertaining sight of six foot athletes flailing at baseballs traveling with the flight path of a drunken small-nosed bat.  But rather because he was drafted in 1996 in the 1st round by the Texas Rangers, and only during his physical workup was it discovered that he was missing a key ligament in his arm.  The Ulnar Collateral Ligament (UCL), to be exact.  Without which, it is assumed, a pitcher cannot pitch. Continue reading →

When a grand old scientist talks, you listen: Maynard Olson and Genomic Medicine

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All opinions are my own and do not necessarily reflect those of Novo Nordisk.

Last night I had the great opportunity to hear Maynard Olson give a public lecture on Genomic Medicine.  As one of the founders of the Human Genome Project, he’s been around in a pivotal role for much of the revolution in our understanding of the genome.  A revolution, as he himself points out, that we are still just beginning.

He gave his speech as part of the UW Genome Sciences Department’s summer lecture series, and spoke to a packed auditorium about how the information we are learning about the genome has implications for diagnostics, therapeutics, and public policy.  I’ve heard Maynard speak before, and he’s always refreshingly down-to-earth, candid and measured in his descriptions and comments.  Not for him are flights of speculation or hyperbole, and he actually ended his talk with a call to stop the hype.  As he said, “The product is solid.  It doesn’t need hype.”  Maynard, who is slim, with a fringe of red hair that’s silvering at the sides (kind of like Reed Richards), does not look at all near his age of about seventy years. Continue reading →

Nothing but nets: applying network theory to the workplace

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All views are my own and do not necessarily reflect those of Novo Nordisk.

For another view on networks and innovation, see this post from Innovation Crescendo.

The metaphor of the healthy workplace has been around long enough that it’s more or less one of those catchphrases business types throw out, like “getting the right people on the bus,” (hat tip to Jim Collins).  And like a lot of memes, “healthy workplace” sticks around because it holds an element of truth in it.  Organizations recognize the value of having a workplace that allows workers to thrive, grow and create.  Because of this, a number of methods have been proposed and are in use for evaluating how healthy an organization is.

I’d like to propose one more.  From working on genomics and transcriptomics, I’ve learned the value of looking at networks of molecules as one way to understand human health, and I’ve been thinking about how the concepts of using networks to measure health could be applied outside of biology.  Specifically, can we apply network theory to help monitor the health of a workplace?

We know, instinctively, that any workplace with more than one employee forms a network at a lot of different levels.  The more employees, the greater the complexity.  This is one of the most important things to us about where we work, isn’t it–the interactions we have on a daily basis?  For many individuals, one of the main perks of work is the chance to spend time and do productive things with like-minded, skilled people.  In knowledge-based industries especially, I think this is one of the most important things for the creative and the talented.

Given this, it’s possible to imagine that characterizing the network itself can be useful.  Biomarkers are routinely employed in biomedical research.  The network formed by the people at work may be a biomarker of organizational health.  It may be the expression of the overall robustness of the organization, just like the phenotype of a person is the ultimate expression of all the biological and chemical networks functioning inside her.  Step one, of course, is figuring out what that network looks like Continue reading →

3D printers, DIY Bio, French bistros and one possible future path for drug development

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All opinions are my own and do not necessarily reflect those of Novo Nordisk

The Long Tail is Everywhere There’s Information

Several years ago I happened upon Chris Anderson’s great book The Long Tail.  He wrote about the amazing changes that were taking place in commerce because of the digitization and electronic dissemination of information.  Mix incredibly cheap (essentially free) data storage with the Internet and reasonable bandwidth, throw in the power of search and individual customization algorithms, and suddenly business models no longer had to rely on bulk consumption and the generation of popular hits.

The first industries to feel the change were in entertainment:  music, movies, books, where having a physical copy was once necessary to enjoy Madonna, Star Wars, or Carl Hiaasen’s latest thriller.  Digitization turned that upside down.  It became clear that what we’re really paying for is information, and it’s a lot harder for the entertainment industry (or any industry) to keep control over the dissemination of information than when they sold that information packaged in shiny plastic discs.

Anderson also described how in this digital world, and aided by the powers of personalized search, niche markets could not only survive but thrive.  Once, something like Tuvan Throat Singing was a niche musical form that you might have heard of on a trip to Siberia, but you’d have had no luck finding a CD at your local Tower Records (remember them?).  Now, you can not only find several tracks from iTunes or Amazon, you’ll also get suggestions for what else you might like based on your fondness for overtone singing.  Since it costs Amazon basically nothing to store the music and associated information, they can afford to have it available for the 20 people who might want to buy it.  Tally that up across all the niches in the world and it’s a hefty sum.

This is pretty neat.  But it’s still uncertain how the business of entertainment will shake out financially and logistically among the producers, distributors and promoters.  I’m not real fond of chaos like that in my professional life, and for a long time felt secure that my job–drug development scientist–was not in danger of becoming part of a long tail phenomenon.  Only now I’m not so sure. Continue reading →