Tag Archives: science

The Future of Academic Research

Yesterday, Nature – one of the worlds premier scientific journals recognized University of British Columbia scientist Rosie Redfield as one of the top 10 science newsmakers of 2011.

The reason?

After posting a scathing attack on her blog about a paper that appeared in the journal Science, Redfield decided to attempt to recreate the experiment and has been blogging about her effort over the past year. As Nature describes it:

…that month, Redfield took matters into her own hands: she began attempting to replicate the work in her lab at the University of British Columbia in Vancouver, and documenting her progress on her blog (http://rrresearch.fieldofscience.com).

The result has been a fascinating story of open science unfolding over the year. Redfield’s blog has become a virtual lab meeting, in which scientists from around the world help to troubleshoot her attempts to grow and study the GFAJ-1 bacteria — the strain isolated by Felisa Wolfe-Simon, lead author of the Science paper and a microbiologist who worked in the lab of Ronald Oremland at the US Geological Survey in Menlo Park, California.

While I’m excited about Redfields blog (more on that below) we should pause and note the above paragraph is a very, very sad reminder of the state of affairs in science. I find the term “open science” to be an oxymoron. The scientific process only works when it is, by definition, open. There is, quite arguably, no such thing as “closed science.” And yet it is a reflection of how 18th century the entire science apparatus remains that Redfields awesome experiment is just that – an experiment. We should celebrate her work, and ask ourselves, why is this not the norm?

So first, to celebrate her work… when I look at Redfields blog, I see exactly what I hope the future of scientific, and indeed all academic research, will look like. Here is someone who is constantly updating their results and sharing what they are doing with their peers, as well as getting input and feedback from colleagues and others around the world. Moreover, she plays to the mediums strengths. While rigorous, she remains inviting and, from my reading, creates a more honest and human view into the world of science. I suspect that this might be much more attractive (and inspiring) to potential scientists. Consider, these two lines from one of her recent posts:

So I’m pretty sure I screwed something up.  But what?  I used the same DNA stock tube I’ve used many times before, and I definitely remember putting 3 µl of DNA into each assay tube.  I made fresh sBHI + novobiocin plates using pre-made BHI agar,, and I definitely remember adding the hemin (4 ml), NAD (80 µl) and novobiocin (40 µl) to the melted agar before I poured the plates.

and

UPDATE:  My novobiocin plates had no NovR colonies because I had forgotten to add the required hemin supplement to the agar!  How embarrassing – I haven’t made that mistake in years.

and then this blog post title:

Some control results! (Don’t get excited, it’s just a control…)

Here is someone literally walking through their thought processes in a thorough, readable way. Can you imagine anything more helpful for a student or young scientist? And the posts! Wonderfully detailed walk throughs of what has been tried, progress made and set backs uncovered. And what about the candor! The admission of error and the attempts to figure out what went wrong. It’s the type of thinking I see from great hackers as well. It’s also the type of dialogue and discussion you won’t see in a formal academic paper but is exactly what I believe every field (from science, to non-profit, to business) needs more of.

Reading it all, and I’m once again left wondering. Why is this the experiment? Why isn’t this the norm? Particularly at publicly funded universities?

Of course, the answer lies in another question, one I first ran into over a year ago reading this great blog post by Michael Clarke on Why Hasn’t Scientific Publishing Been Disrupted Already? As he so rightly points out:

When Tim Berners-Lee created the Web in 1991, it was with the aim of better facilitating scientific communication and the dissemination of scientific research. Put another way, the Web was designed to disrupt scientific publishing. It was not designed to disrupt bookstores, telecommunications, matchmaking services, newspapers, pornography, stock trading, music distribution, or a great many other industries…

…The one thing that one could have reasonably predicted in 1991, however, was that scientific communication—and the publishing industry that supports the dissemination of scientific research—would radically change over the next couple decades.

And yet it has not.

(Go read the whole article, it is great). Mathew Ingram also has a great piece on this published half a year later called So when does academic publishing get disrupted?

Clarke has a great breakdown on all of this, but my own opinion is that scientific journals survive not because they are an efficient means of transmitting knowledge (they are not – Redfield’s blog shows there are much, much faster ways to spread knowledge). Rather journals survive in their current form because they are the only rating system scientists (and more importantly) universities have to deduce effectiveness, and thus who should get hired, fired, promoted and, most importantly, funded. Indeed, I suspect journals actually impede (and definitely slow) scientific progress. In order to get published scientists regularly hold back sharing and disclosing discoveries and, more often still, data, until they can shape it in such a way that a leading journal will accept it. Indeed, try to get any scientists to publish their data in machine readable formats – even after they have published with it -it’s almost impossible… (notice there are no data catalogs on any major scientific journals websites…) The dirty secret is that this is because they don’t want others using it in case it contains some juicy insight they have so far missed.

Don’t believe me? Just consider this New York Times article on the break throughs in Alzheimer’s. The whole article is about a big break through in scientific research process. What was it? That the scientists agreed they would share their data:

The key to the Alzheimer’s project was an agreement as ambitious as its goal: not just to raise money, not just to do research on a vast scale, but also to share all the data, making every single finding public immediately, available to anyone with a computer anywhere in the world.

This is unprecedented? This is the state of science today? In an era where we could share everything, we opt to share as little as possible. This is the destructive side of the scientific publishing process that is linked to performance.

It is also the sad reason why it is a veteran, established researcher closer to the end of her career that is blogging this way and not a young, up and coming researcher trying to establish herself and get tenure. This type of blog is too risky to ones career. Today “open” science, is not a path forward. It actually hurts you in a system that prefers more inefficient methods at spreading insights, research and data, but is good at creating readily understood rankings.

I’m thrilled that Rosie Redfield has been recognized by Nature (which clearly enjoys the swipe at Science – its competitor). I’m just sad that the today’s culture of science and universities means there aren’t more like her.

 

Bonus material: If you want to read an opposite view, here is a seriously self-interested defensive of the scientific publishing industry that was totally stunning to read. It’s fascinating that this man and Michael Clarke share the same server. If you look in the comments of that post, there is a link to this excellent post by a researcher at a University in Cardiff that I think is a great counter point.

 

Ada Lovelace Day – On Dr. Connie Eaves

For those who don’t know: Today – October 7th – is Ada Lovelace Day. It’s a day where you “share your story about a woman — whether an engineer, a scientist, a technologist or mathematician — who has inspired you to become who you are today.”

It would be remiss for me not to blog about Dr. Connie Eaves. For anyone who thinks I travel a lot, work long hours, or have a passion for evidence and data, I am really just a pale shadow when compared to this inspiring and globally recognized cancer researcher. For those not familiar with her – which is probably anyone outside the field of cancer research and not an avid reader of the journal Blood – you can catch her bio on Wikipedia here.

She is, of course, also my mom.

Obviously, if you are a woman (or a man) interested in getting into science – particularly human biology and stem cell research – I would point you to my mother (and father) as people to get to know, but for me her inspiration is much simpler. At a basic level, there are two invaluable gifts my mother has given me, which I feel are particularly salient to her scientific achievements.

The first, and most important, was the building blocks of critical thinking: To break down an argument and understand it from every angle, as well as dissect the evidence embedded within it. These lessons were hard ones. I learned a lot of it just through observation, and sometimes – more painfully – from trying to engage her in debate. I’ve seen graduate students tremble in fear about engaging my mother in debate. While my victories have been few, I’ve been doing it since probably the age of five or earlier, and it has helped shape my brain in powerful ways in which, I suspect, many masters or doctoral students would happily travel around the world to be exposed to. I am exceedingly lucky.

The second gift my mom bestowed me is her work ethic and drive. I have grown up believing that working for 12 hours, 7 days a week may actually be normal behaviour. There is good and bad in taking on such norms. Neither one of us probably thinks it is healthy when we skip eating all day because we zone out into our work. But that intensity has its upsides, and I’m grateful to have been exposed to it. Indeed, I’d like to think I work hard, but standing next to her, I still often just feel lazy.

I mention these two traits not just because they have had such a great impact on me, but also because I think they’re a reflection of what extraordinary skills were required by my mother to be a successful woman scientist embarking on a career in the 1960s. The simple fact is that in that era, as much as we’d like to think it was not true, I suspect that to be a women scientist – to get on tenure track – you had to be smarter and work harder than almost anyone around you. It is one reason why I think the women scientists of that generation are generally so remarkable. The sad truth is: They had to be.

The happy upside is that for me, purely selfishly, is I got the benefit of being raised by someone who survived and thrived in what I imagine was at times a hostile environment to women. Paradoxically, the benefits I enjoyed are those I would wish on any child in a heartbeat, while the asymmetric expectation are those I would wish on no one.

Happy Ada Lovelace mom.

How Science Is Rediscovering "Open" And What It Means For Government

Pretty much everybody in government should read this fantastic New York Times article Sharing of Data Leads to Progress on Alzheimer’s. On one hand the article is a window into what has gone wrong with science – about how all to frequently a process that used to be competitive but open, and problem focused has become a competitive but closed and intellectual property driven (one need only look at scientific journals to see how slow and challenging the process has become).

But strip away the talk about the challenges and opportunities for science. At its core, this is an article is about something more basic and universal. This is an article about open data.

Viewed through this lens it is a powerful case study for all of us. It is a story of how one scientific community’s (re)discovery of open principles can yield powerful lessons and analogies for the private sector and, more importantly the public sector.

Consider first, the similarities in problems. From the article:

Dr. Potter had recently left the National Institutes of Health and he had been thinking about how to speed the glacial progress of Alzheimer’s drug research.

“We wanted to get out of what I called 19th-century drug development — give a drug and hope it does something,” Dr. Potter recalled in an interview on Thursday. “What was needed was to find some way of seeing what was happening in the brain as Alzheimer’s progressed and asking if experimental drugs could alter that progression.”

Our government’s are struggling too. They are caught with a 20th-century organizational, decision-making and accountability structures. More to the point, they move at a glacial speed. On the one hand we should be worried about a government that moves too quickly, but a government that is too slow to be responsive to crises or to address structural problems is one that will lose the confidence of the public. Moreover, like in healthcare, many of the simpler problems have been addressed. citizens are looking for solutions to more complex problems. As with the scientists and Alzheimer’s we may need new models to speed the process up for understanding and testing solutions for these issues.

To overcome this 19th century approach – and achieve the success they currently enjoy – the scientists decided to do some radical.

The key to the Alzheimer’s project was an agreement as ambitious as its goal: not just to raise money, not just to do research on a vast scale, but also to share all the data, making every single finding public immediately, available to anyone with a computer anywhere in the world.

No one would own the data. No one could submit patent applications, though private companies would ultimately profit from any drugs or imaging tests developed as a result of the effort.

Consider this. Here a group of private sector companies recognize the intellectual property slows down innovation. The solution – dilute the intellectual property, focus on sharing data and knowledge, and understand that those who contribute most will be best positioned to capitalize on the gains at the end.

Sadly this is the same problem faced within governments. Sometimes it has to do with actual intellectual property (something I’ve recently argued our governments should abandon). However, the real challenge isn’t about about formal rules, it is more subtle. In complex siloed organizations where knowledge is power the incentives to maximize influence are to not share knowledge and data. Better to use the information you have strategically, in a limited fashion, to maximize influence. The result, data is kept as a scarce, but strategic asset. This is a theme I tackled both in my chapter in Open Government and in blog posts like this one.

In short, the real challenge is structural and cultural. Scientists had previously existed in a system where reputation (and career advancement) was built by hoarding data and publishing papers. While the individual incentives were okay, collectively this behavior was a disaster. The problem was not getting solved.

Today, it would appear that publishing is still important, but there are reputational effects from being the person or group to share data. Open data is itself a currency. This is hardly surprising. If you are sharing data it means you are doing lots of work, which means you are likely knowledgeable. As a result, those with a great deal of experience are respected but there remains the opportunity for those with radical ideas and new perspectives to test hypothesis and gain credibility by using the open data.

Unsurprisingly, this shift wasn’t easy:

At first, the collaboration struck many scientists as worrisome — they would be giving up ownership of data, and anyone could use it, publish papers, maybe even misinterpret it and publish information that was wrong.

Wow, does that sound familiar. This is invariably the first question government officials ask when you begin talking about open data. The answer, both in the scientific community and for government, is that you either believe in the peer-review process and public debate, or you don’t. Yes, people might misrepresent the data, or publish something that is wrong, but the bigger and more vibrant the community, the more likely people will find and point out the errors quickly. This is what innovation looks like… people try out ideas, sometimes they are right, sometimes they are wrong. But the more data you make available to people the more ideas can be tested and so the faster the cycle of innovation can proceed.

Whether it is behind the firewall or open to the public, open data is the core to accelerating the spread of ideas and the speed of innovation. These scientists are rediscovering that fact as our some governments. We’ve much to learn and do, but the case is becoming stronger and stronger that this is the right thing to do.

Articles I'm Digesting 15/12/2009

Here are some pieces I’ve been reading of late:

You Can’t Handle the Truth by Mark Pothier in the Boston Globe

A great piece about how the classification of drugs used by most Western countries is completely divorced from how much harm those drugs cause. This isn’t surprising, but as the evidence begins to mount regarding which drugs are actually harmful (read alcohol, cocaine or heroine) versus those which are significantly less harmful (read Ecstasy or LSD) the question will increasingly emerge – will science ever inform our policies around managing these types of substances. Indeed, it is disturbing (and, er… sobering) to once again see the only  substance I use the list – alcohol – be put in such a stark and negative light.

At some point a real conversation about drugs is going to occur in the United States – I just hope it is sooner rather than later as it will have a profound effect on effectively we can deal with the tragic situation we have around substance abuse this side of the border.

Fla. Court Tells Judges and Lawyers to “Unfriend” Each Other (the AP)

Always fascinating to see how different fields respond to social networking. In this case a Florida…

…committee ruled Nov. 17 that online “friendships” could create the impression that lawyers are in a special position to influence their judge friends.

This is a great example of how social networking can cause some professions to actually become less transparent and, I would argue, harms the long term credibility of the institution. Notice here that the committee isn’t ruling that judges and lawyers can’t be friends, they are ruling that it would be harmful if the public could see that they are friends. So, in essence, if being a friend compromises the judgment of a judge, we solve that by preventing the public from seeing that the conflict could exist, rather than dealing with the conflict. Weird.

The last line is priceless:

McGrady, who is sending a copy of the ruling to the 69 judges in his circuit, said this potential conflict of interest is why he doesn’t have a Facebook page.

“If somebody’s my friend, I’ll call them on the phone,” he said, chuckling.

Errr, right. Good to keep it all in the old boys network where those on the inside know where the conflict may lie, but there is not digital trail or map that might allow the public to be better informed… Oh, and you’re the last generation that will only “pick up the phone” so this solution has, at best, a 20 year shelf life to it.

The Killer App of 1900 by Glenn Fleishman in Publicola

As some readers know, I’m a big fan of historical examples that show we are experiencing similar pressures, transformations, evolutions as experienced in the past. Part of it is the historian in me, part of it is how it helps ease the minds of those concerned or intimidated by change. There are, occasionally, genuinely new things that appear under the sun – but often those of us interested in technology and social change are too quick to scream “This is new! It changes everything!” Moreover, it does a disservice to our efforts often making people more skeptical, resistant and generally conservative towards the perceived change. Still more importantly, the past often sheds light on how power and influence created by a new technology or system may diffuse itself – who will be the winners/losers and the resisters.

In this context this article is a priceless example of the type of writing I wish I did more of.

The Score: Advice to Young Composers by Annie Gosfield in the New York Times

While written as sounds advice for composers, this is (as the friend who sent it to me said) sounds advice for policy wonks or, in my opinion, bloggers as well. (It’s actually just sounds advice for life).

A couple of credos in the piece that I hope my work, and this blog lives by:

Take your work seriously, but don’t take yourself too seriously: Hope that is evident in my writing style.

Be willing to put yourself and your music on the line: Try to do that everyday here on the blog.

Don’t fear rejection: Something a blog is really good at teaching you.

A couple of credos in the piece I know I struggle with:

Don’t assume you know what’s accessible to the audience and what isn’t: Although counter to what the piece says, I occasionally run into a friend who says “I had NO idea what you were talking about in X blog post.” It is crushing to hear – but also really good. I do want to challenge readers but I also want to be accessible. Do let me know if I ever get to a place where a newbie is going to be totally lost.

Details count: So, er, anyone who reads my blog regularly knows that I have the occasional typo in a post, here or there… Blogging longish pieces four times a week is draining, and so I don’t proof as much as I could (plus it is hard to see one’s own errors). But I could do better.

Hope you enjoy these pieces as much as I did!

Stem Cell Charter Sign & Share Rally Begins!

Why did I sign The Stem Cell Charter?

Yes, I’ve been really impressed with the launch and the associated campaign. Yes, my parents are cancer researchers and I (literally) grew up in lab. Yes, the website and videos are beautifully done. Yes, the Charter is well crafted, balancing both the opportunities created, and the rigor demanded, by science with the ethics that should guide all human endeavors. And yes, I believe in both the potential of stem cell research to create new cures and medical treatments and improvements to the quality of our lives this will foster.

But I signed the charter because at my core, I believe science to be one of the simplest, noblest, and purest pursuits available to humanity. It is the one endeavor in which, I believe, we come closest to understanding the unknowable truth about who we are, where we are, and how we got here. Stem cell research is an important part of that endeavor. The choice isn’t between banning it or not. The choice is do we conduct this research the way we should all science: openly, ethically, and in pursuit of the truth. This is what the Charter says to me.

But then, that’s just my reason. I hope you’ll have your own. If you do, I also hope be part of The Stem Cell Charter Sign & Share Rally that is running from now until Saturday. So check out the site and sign the charter! (copied below).

If you are really keen you can also:

  • Learn more about the Stem Cell Charter and stem cell research. (The side has some pretty cool content including 12 mini-videos by clicking on “Renew the World”. Trust me – the scientists are real, not actors.)
  • Digg the site
  • Post links on facebook (and become a fan of The Stem Cell Charter)
  • Tweet using the hashtag #stemcellcharter (and follow @stemcellcharter)
  • Blog about why you’ve signed the Charter and why you think others should (like I have)

The Charter:

The Stem Cell Charter maintains that stem cell science has the potential to revolutionize the practice of medicine, develop treatments for diseases and create unprecedented hope for humanity.

The Stem Cell Charter affirms that, “[e]njoyment of the highest attainable state of health is one of the fundamental rights of every human being without distinction of race, religion, political belief, economic or social condition.” – WHO, Constitution (1946)

To that end, the Stem Cell Charter upholds the following principles:

  • Responsibility to maintain the highest level of scientific quality, safety and ethical probity
  • Protection of citizens from harm and the safeguarding of the public trust and values
  • Intellectual Freedom to exchange ideas in the spirit of international collaboration
  • Transparency through the disclosure of results and of possible conflicts of interest
  • Integrity in the promotion and advancement of stem cell research and therapy for the betterment of the welfare of all human beings

Endorsing the Stem Cell Charter is a collective call to action. By signing the Charter, we commit as individuals and organizations:

  • To affirm the importance of stem cell science for humanity
  • To advance stem cell science and the principles articulated in the Charter
  • To disseminate the Stem Cell Charter
  • To lend our voice, time or other resources to advancing stem cell science as part of the Stem Cell Charter community, the Foundation or other related stem cell organizations or groups
  • The Day my Universe Changed

    burke-universeLast night I re-watched the first episode of James Burke’s 1985 history/science series, The Day the Universe Changed. If you’ve never had a had a chance to watch it, find it in your local library or watch it on Youtube (thank you Gary C for the link) you won’t regret it.

    James Burke is a personal hero of mine. I fell in love with his work in Grade 9 when I stumbled across his shows on The Learning Channel. I even emailed with him in my second year of undergrad in the hopes of securing a summer job (I wasn’t successful).

    There are so many things I learnt from Burke that have stayed with me over the past 2 decades but three things really stuck out as I re-watched the first episode.

    First, I’ve always admired his ability to take incredibly complex ideas and make them not only easy to understand, but fun and engaging. Part of it is his passion: Here is a man with a sharp mind, a glint in his eye, and a heart in love with his chosen subject. But watching the episode, it is obvious that the script is meticulously planned. So as Burke hops around the world, every word, every scene, every prop, helps advance the idea and narrative he is conveying. Had TED talks been available over the internet in 1985, I think James Burke would have been the master TED talk presenter (and more of a household name today). I spend a good part of my life trying to convey ideas, and it’s fun to go back and see a master at work.

    Second, James Burke is the first person who made me consciously comfortable with complexity. I always loved history (I ultimately majored in it) but until I met Burke history was always conveyed in a nice neat linear fashion. Burke tore that notion up. He weaves together complicated tapestries (which in the medium of television is no small feat) of not just science, history and social change, but also of luck, chance and misfortune to help paint a picture of how we ended up being both who we are, and where we are. Reflecting on my most recent talk on the future of government and on a recent blog post, I’ve frequently talked about how:

    The biggest problem in predicting the future isn’t envisaging what technologies will emerge – it is forecasting how individuals and communities will respond to these technologies. In other words I often find people treat technology as a variable, but social values as a constant.

    Watching Burke yesterday, I realized that 20 years ago he shared this idea with me first. If I’m comfortable with the complexity of this type of thinking today, it’s because he’s given me two decades to first get comfortable, and then mature intellectually, with it.

    So if you are interested, go find a copy of The Day the Universe Changed. It is a wonderful defense of curiosity and asking questions, no matter what powers or issues that puts you at odds with. It’s that curiosity that Burke made me aware of in myself, and that today fuels and motivates me.

    Thank you James.

    How bad design led to a lost decade

    First, I’m away on vacation (hence the scarce number of posts) and am consumed writing a few chapters for a couple of books that I’m contributing to – more on those in the near future I hope.

    In the interim, I became profoundly depressed this morning after reading the passage below. I’m certain that history will look back at the Bush presidency as a “lost decade” when not only did the economy go off the rails and America’s standing in the world plummeted, but hundreds of thousands of lives were lost and billions were wasted in Iraq, human rights were hurled decades backwards and the benefits and progress of work in the humanities and sciences were put on hold (and in many cases, simply wasted).

    Thinking these thoughts can itself be depressing. But this excerpt made it worse:

    If you’re still unconvinced that design can have consequences beyond the carport and cutting board, point your memory back to the 2000 U.S. presidential elections and the thirty-six-day snarl over whether Al Gore or George W. Bush won the most votes in Florida. That election and its aftermath may seem like a bad dream today. But buried in that brouhaha was an important, and mostly ignored, lesson…

    …According to an exhaustive examination of all of Florida’s ballots that several newspapers and academics conducted a year after the election-and whose findings were largely lost amid the coverage of the September 11th, 2001, terrorist attacks and utterly forgotten after Bush’s 2004 reelection-what determined who won the U.S. presidency was the infamous butterfly ballot that voters in Palm Beach county used to mark their choice for President. In Palm Beach County – a heavily Democratic enclave populated by tens of thousands of elderly Jewish voters – ultraconservative fringe candidate Pat Buchanan recieved 3,407 votes, three times as many votes as he did in any other county in the state. (According to one statistical analysis, if the voting pattern of the state’s other sixty-six counties had held in Palm Beach, Buchanan would have won only 603 votes.) What’s more, 5,237 Palm Beach County voters marked ballots for both Al Gore and Pat Buchanan, and therefore had their ballots invalidated. Bush carried the entire state by 537 votes.

    Less well known is the ballot in Duval County in which the presidential ballot showed five candidates on one page and another five candidates on the next page, along with instructions to “vote every page.” In that county, 7,162 Gore ballots were tossed out because voters selected two candidates for President. Had the instructions been clearer, Duval County, too, would have provided Gore the margin of victory.

    A Whole New Mind: Why Right-Brainers Will Rule the Future, Daniel H. Pink

    Design does matter. In this case, poor design costs America (and much of the world) a decade of progress and, possibly, countless billions (if not trillions).