Category Archives: Randomness

Finding an Alka Seltzer for the oceans

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All opinions are my own and do not necessarily reflect those of Novo Nordisk
Some time ago I wrote an article for Real Change (reposted here) about research being done at the University of Washington to understand the effects of ocean acidification due to rising atmospheric carbon dioxide levels.  The rising pH of the oceans is another one in my list of things we don’t worry enough about with climate change but really should.  Like the bees.  It’s such a seemingly tiny, subtle thing.  The measured decrease in pH of maybe 0.1 units is due to ocean waters absorbing atmospheric CO2 and the resulting conversion of some of that to carbonic acid.  Seems small but it’s really a big deal.
Scientists have documented apparent effects of ocean acidity on coral reefs and oysters, among other organisms (abstracts from links; articles behind paywalls), and while oyster farmers can try to add antacids to their spawning beds, the oceans as a whole are a bit large for a local solution.  Which is why I was excited to see the Paul Allen Family Foundation post the current submissions to their Ocean Challenge (HT @deirdrelockwood).
Let me provide a disclaimer that I have not read most of these proposals in depth.  However, scanning through the titles and sampling a few in greater detail, it’s clear that the Ocean Challenge has prompted a number of groups to come up with ideas about how to try and monitor, test, and mitigate the effects of ocean acidification, at least at the local level and in some cases on a grander scale.  The proposals are available online for public comment, and finalists selected in September.
There are a couple of things to really like about this.   All the proposal summaries are devoid of names and affiliations, which may lead to more unbiased evaluations by public commentators.  This is something that’s been debated for years with respect to other granting agencies like the NIH.  Another great thing is that this is open–anyone can apply and everyone’s ideas are out there for others to learn from, debate, and expand upon.  I’m a fan of open source science, and transparency, and this feels like it’s in that vein.  And last, this is really a big problem.  Not to say government agencies aren’t funding and studying this, but as we’ve seen with other private non-profit foundations like the Gates Foundation, there is a third way beyond government and private industry to try and effect policy and make changes.  I hope for success from this effort.  Because I would really miss oysters.

Are Biopharma reagent companies sitting on a pile of gold (or at least poptarts)?

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

The recent news about the United States Government monitoring a great deal of both general and specific electronic data has had one beneficial outcome (or at least, one I feel is beneficial):  it has made more people aware of what can actually be done with data, and also that we’re leaving massive amounts of personal data out there that can be traced to the behavior of individuals or organizations.  A few months ago, the Seattle Times published an article describing the explosion of big data and how that can be leveraged in so many ways.

This led me to speculate, in a very out-there kind of way, about what kinds of data Biopharma companies produce and whether there’s any hidden value in that.  Now, certainly companies are very careful about communicating information to the outside world.  Contracts with collaborators routinely contain embargo clauses, and presentations and posters are carefully vetted by legal and communications departments.  So companies would appear to be covered there.  But what kinds of data are out there that might be available, maybe not freely, but in potentia, to an interested audience?

Let me digress for a moment about mergers.  Biopharma over the last few years has seen a flurry of merger and acquisition activity.  The big pharma deals, like Pfizer/Wyeth, and Merck/Schering-Plough, have gotten big press, but there has also been a lot of consolidation among reagent suppliers.  To take one example, I’ve shamelessly taken Life Technologies’ merger history off of Wikipedia and condensed it into this table (after the jump): 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 →

Why everyone should worry (more) about the bees

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

Among my personal top list of things people really should be more worried about with respect to how we’re changing the environment, the decline of bees is close to number one.  On some days, like when I’m biting into a delicious Rainier cherry or a luscious peach, the decline of bees is number one.    And I’m not saying this topic hasn’t gotten any press or concern.  On the contrary, there’s been plenty.  I just also think it should have more.

So imagine the jolt to my already heightened sense of worry when I saw the following two studies.  This one, in Nature (abstract only, article behind a paywall), puts forth a theoretical model of what happens when a species goes “functionally extinct.”  By this, the authors mean the point at which the number of members of a given species in an ecosystem declines to the point that other species are affected and may themselves go fully extinct.  It turns out that in interconnected food webs, as a given species declines in numbers, it affects other species’ overall survival as well, and that most often the species going really and truly extinct is not the one initially declining.

I think of this situation as being kind of like playing in a massively multiplayer online role-playing game like Star Wars: The Old Republic, and you’re in a team with several others, each of whom has his or her role.  Often the healer of the party gets damaged quickly in a fight, but they’re not the first one to go down.  Instead, it’s the damage-dealing specialists who find themselves getting beat up and dying when the healing falters.  The team, the network, relies on every member functioning fully to succeed, and reducing performance by one part of the team can have unintended consequences.

Well, that was a tortured analogy.

But the point with respect to bees is how just the decline of bee populations alone may be having cascading effects on the ecosystems in which they operate.

Another take on the importance of different species and diversity in networks comes from this study in the Proceeding of the National Academy of Sciences (USA) (abstract only, article behind a paywall).  In this situation, the researchers tested the idea that plant community and insect networks are robust enough to survive the loss of individual species.  They located subalpine meadow plots and carefully removed all members of a single pollinator species and asked what would happen.  Network robustness theory would suggest other pollinators would take the place of the removed species, which previously served a specific niche.  And this happened.  However, the overall health of the plant community nevertheless appeared potentially threatened since this meant pollinators carried more types of pollen, leading to less efficiency in pollinating any given plant species.

These studies are just two of many that describe the unexpected and unintended consequences of changes in ecosystem communities.  All kinds of changes.  Like the decline of frogs and other amphibians, which I also worry about.  My personal bias towards worrying about bees probably stems from my perception of the crucial role they play in so many functions, both for humankind in specific and ecosystems in general.  The Nature paper also suggests the scary thought that we might be missing the forest for the bees, and the real impact of bee declines has already happened in the extinction of other, interconnected species which we may never know about, because they might already be gone.

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 →