Category Archives: Big Data

What would you want to do with genome sequence data?

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

In the same issue of Nature that reported the HeLa sequence and the NIH agreement, Martin Bobrow of the University of Cambridge wrote a column discussing how we as a society choose to balance individual privacy and public good that arises from making data gathered from private samples public.

We are entering a strikingly different period of biological and biomedical research, as a number of different areas of research and technology are reaching a critical point of cross-fertilization.  Moore’s law has resulted in computers of amazing power that can analyze really stupendous amounts of data.  I was at the Seattle Museum of History and Industry recently, and in one of their displays they showed a 1980 IBM PC, and while showing it to my son, I pulled out my smartphone and told him that my phone today is just as powerful as that computer was.  Of course, I was wrong.  My phone is actually about 2.5 orders of magnitude more powerful than that PC. Continue reading →

Gaming to help beat cancer

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

Plants versus Zombies 2: It’s About Time just came out.  My son spent a significant fraction of his weekend playing it on my iPad.  Okay, fine, I did too.  It’s a lot of fun, it challenges (but not too much) and it teaches you facts like, uh, like that Egyptian society in the past had a real fascination with pyramids.

So it’s not the most educational of games.

Which is why I was stoked to see the writeup of Re-Mission 2 in FierceBiotechIT.  This game takes elements of cancer treatment and places them in the context of a game that both educates patients undergoing cancer treatment as well as provides them a way to feel more in control of their situation.  Version 2 also builds on the impact of the first Re-Mission game, which showed success in improving adherence of patients to their treatment regimens.  Adherence is an important element of medical treatment and trying to make sure people take their medicines is an ongoing problem as we try to improve the efficiency of our healthcare systems.

In addition to behavioral metrics being changed by Re-Mission, functional Magnetic Resonance Imaging (fMRI) also showed that playing the game activated brain areas associated with motivation–again, tying gameplay to elements of adherence.  Some brain region activations also correlated with subject described positive and improved attitudes towards chemotherapy after gameplay. Continue reading →

Internet access is a public (and private) health issue

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

If the Founding Fathers had lived today, they would surely have included internet access as one of our inalienable rights.  No, scratch that, because if they had lived today they would have used Google Docs to crowdsource the Declaration and the result would probably have been much more generic and middle of the road than it actually is.  Also, the Declaration would also have been limited it to about 500 words so readers wouldn’t get bored and surf somewhere else, and it would have had embedded GIFs. Preferably animated.

Still, the ability to access the internet and everything that comes with that is, if not a right, an incredible advantage.  So I was stunned when I read in the Seattle Times the other day that a significant fraction of people in the US–about twenty percent–have little to no internet connection, although those numbers have recently begun to creep up, presumably due to smartphone uptake.   But of course, being a good Seattlelite with a liberal bent, my next reaction was to say, well, let’s not rush to judgement or conclusions.  Maybe those people just don’t want the internet.  Not that there’s anything wrong with that…

Except the article goes on to say that while seniors generally did not feel they were missing anything, the majority of other respondents did feel they were missing something important and were being left behind because of their limited access.  So it’s not a life decision; it’s a question of cost, access and education. Continue reading →

Enter citizen science

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

h/t to @engagedethics for the heads up.

What do you think of when you think of citizen science?  Maybe dads buying Geek Dad and helping their kids build Lego robots that can manipulate a lego binary clock.  Maybe people tracking their health, thoughts, bodies, or other things in a really granular way in an effort to get at their quantified self.  Maybe hobbyists building and flying drones to sample atmospheric particle levels or track neighborhood traffic patterns.  Maybe patients groups banding together and funding research into cures, like the Cystic Fibrosis Foundation did with Kalydeco.  Maybe birdwatchers helping researchers track the migration patterns and populations of North American birds.  Maybe it’s something else, something you know about or have heard about or are planning to do right now.  Choose any or all of the above and you’re completely right.

Because citizen science, like a lot of movements these days, isn’t something legislated or codified or directed from on high. It’s something organic and crowd-based and bottom up, and it’s going on everywhere.

This is the world that’s being enabled by technology.  Whether it’s 3D printing, DIY Bio, computer modeling, personal monitoring or other kinds of tools, the barriers to experimentation are falling rapidly, and interest in figuring stuff out is on the rise.

The Citizens Science Association has been working on ways to support this new way of doing science.  They’ve been convening groups to look at topics like Governance, Conferences, ways to publish, and ways to communicate via other means.  There will be a webinar on September 17th to report on progress and it sounds like a worthwhile thing to listen to.  I haven’t been involved in the Association, but I’m planning to listen in.  Because technology keeps lowering the barriers to entry, and I’m really excited to see what comes out.

Lack of replication no surprise when we’re studying really complex problems

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

For another nice take on this topic see Paul Knoepfler’s blog post here.

One of the sacred (can I say sacred in reference to something scientific?) tenets of the scientific method is reproducibility.  If something is real and measurable, if it’s a fact of the material world, then the expectation is that the result should be reproducible by another experimenter using the same methods as described in the original report.  One of the most well known (among physicists anyway) examples of irreproducible data is the Valentine’s Day Magnetic Monopole detected by Blas Cabrera back in 1982.  Great experimental data.  Never repeated, and therefore viewed as insufficient proof for the existence of a magnetic monopole.

So it’s troubling that in the past few years there have been numerous stories about the lack of reproducibility for different scientific experiments.  In biomedical science the number of  reports on the difficulty of reproducing results has gotten so great that the NIH has begun thinking about how to confirm and require reproducibility of some kinds of experimental results.  Just a few days ago another field, that of psychological priming, saw the publication of an article that the effects of “high-performance priming,” could not be reproduced.  This is another field undergoing serious questioning about whether/why results don’t reproduce, with commentary from such luminaries as Daniel Kahneman. Continue reading →