What the pot and pain pill overdose study teaches us about ecological fallacies

I am delighted to offer Mind the Brain readers a guest blog written by Keith Humphreys, Ph.D., John Finney, Ph.D., Alex Sox-Harris, Ph.D., and Daniel Kivlahan, Ph.D. Drs. Humphreys, Sox-Harris, and Finney are at the Palo Alto VA and Stanford University. Dr. Kivlahan is at the Seattle VA and the University of Washington.

Follow Professor Humphreys on Twitter @KeithNHumphreys.


Image Credit: Bogdan, Wikimedia Commons
Image Credit: Bogdan, Wikimedia Commons

A team of scientists recently reported that states with laws permitting medical marijuana had lower rates of opioid overdose than states without such laws. In a New York Times essay, two members of the team suggested this state-level association between medical marijuana access and deaths reflects the behavior of individuals in pain:


If enough people opt to treat pain with medical marijuana instead of prescription painkillers in states where this is legal, it stands to reason that states with medical marijuana laws might experience an overall decrease in opioid painkiller overdoses and deaths.


At first blush, saying it “stands to reason” seems, well, reasonable. But in the current issue of the journal in which the study appeared, we point out that the assumption that associations based on aggregations of people (e.g., counties, cities and states) must reflect parallel relationships for individuals is a seductive logical error known as the “ecological fallacy.”


Once you understand the ecological fallacy, you will recognize it in many interpretations of and media reports about science.   Here are some examples that have been reported over the years:



Such differences are counter-intuitive and therefore a bit baffling. If individuals having heart attacks who receive high quality care are far more likely to survive, doesn’t it follow that hospitals that provide higher quality care to larger percentages of their heart attack patients would have substantially lower mortality rates? (Answer: No, their results are barely better). Why don’t patterns we see in the aggregate always replicate themselves with individuals, and vice versa?


The mathematical basis for the ecological fallacy has multiple and complex aspects (our detailed explanation here), but most people find it easiest to understand when presented with a simple example. Imagine two states with 100 people each residing in them, with each state population including a comparable proportion of people in pain. Potsylvania has a loosely regulated medical marijuana system that 25% of residents access. Alabstentia, in contrast, limits access to medical marijuana so only 15% of residents can obtain it.



Medical Marijuana User Medical Marijuana Non-User Totals
Died of Opioid Overdose 2 3 5
Did Not Die of Overdose 23 72 95
Totals 25 75 100




Medical Marijuana User Medical Marijuana Non-User Totals
Died of Opioid Overdose 4 6 10
Did NotDie of Overdose 11 79 90
Totals 15 85 100


Ganja-loving Potsylvania has a lower opioid overdose death rate (5%) than more temperate Alabstentia (10%).   Does this prove that individuals in those states who use medical marijuana lower their risk of opioid overdose death? Nope. In both states, medical marijuana-users are more likely to die of a pain medication overdose than are non-users: 2 of 25 (8%) of marijuana users dying versus 3 of 75 (4%) marijuana non-users dying in Potsylvania; 4 of 15 (26.6%) of marijuana users dying versus 6 of 85 (7.1%) of non-users dying in Alabstentia!


Embracing the ecological fallacy is tempting, even to very bright people, but it must be resisted if we want to better understand the world around us. So, the next time you see a study saying, for example, that politically conservative states have higher rates of searching for sex and pornography on line and want to immediately speculate about why conservative individuals are so hypocritical, pause and remember that what applies at the aggregate level does not necessarily apply to individuals. For all we know, alienated liberals in red states may just be feeling lonely and frustrated.

Understanding Lack of Access to Mental Healthcare in the US: 3 Lessons from the Gus Deeds Story

From “60 Minutes,” CBS Television, January 26th, 2014

Creigh Deeds: There’s just a lack of equity in the way we as a society, and certainly as a government and insurance industry, medical industry, with the way we look at mental health issues.

Scott Pelley: Don’t want to fund it. Don’t want to talk about it. Don’t want to see it.

Sen Creigh Deeds on 60 Minutes
Sen Creigh Deeds on 60 Minutes


Creigh Deeds: Absolutely. That– that’s exactly right. But the reality is, it’s everywhere.





If inadequate access to mental healthcare in the US is a disease, and I would argue that it can certainly be seen that way in terms of the toll it has taken on American society, then medical school did next to nothing to prepare me to understand its causes; or, to deal with them. After 15 years of treating thousands of patients with psychiatric disorders, I have long struggled to concisely understand and articulate the confluence of factors that determine why my patients do (or do not) have access to mental healthcare.

Recently, whilst watching 60 minutes all that changed. From the story of a young man named Gus Deeds, a clear and concise picture emerged of cause and effect, depicting the factors that largely determine whether a patient in need of mental health care is likely to receive that care.

In this segment, Scott Pelley interviewed Virginia State Senator, Creigh Deeds, about his son Gus, who was 24 years old and had been living with serious mental illness.  His struggle culminated, last November, in a tragic ending. The Deeds’ predicament with their son was echoed by other family members of mentally ill children and adults who were also interviewed for this segment.

I was deeply saddened and perturbed by the story and although I had never met any of the people involved and had no inside knowledge of the situation, Senator Deed’s narrative was all too familiar to my ears as a litany of causes for an avoidable tragedy : inadequate mental health resources; resistance to care by the patient; additional obstacles presented by insurance companies, and fragmented treatment options.

Watching the interview, my head reverberated with all the questions I had asked myself when attempting to provide care for patients with serious mental illness.

These were the types of questions that plagued me during the earlier days of my career.  Why am I not able to stop them falling through the cracks in the system? Why do I have to spend so much time persuading insurance companies to pay for their basic care? What am I doing wrong? What can I do better?  Why does the opinion of their loved ones not seem to count?

The causes behind inadequate access to mental health care in the US must be described with a terminology not taught in medical school. They hail from different worlds than the one in which I was trained: the worlds of law, healthcare policy, sociology and the insurance industry.

Gus Deeds and Craig Deeds, 2009
Gus Deeds and Craig Deeds, 2009

If this situation is going to change, the Gus Deeds story provides a tragic, teachable moment for all Americans.

Here are 3 key lessons we can all learn from what happened to the Deeds family.



#1 Despite reforms, mental health care services are inadequate or nonexistent to large segments of American Society

 Access to mental healthcare starts with the premise that, if services are available and there is an adequate supply of services, then the opportunity to obtain health care exists, and a population may ‘have access’ to services. Unfortunately, this assumption of adequate supply cannot be made with regards to services provided by mental health professionals.  There is a shortage of mental health professionals in the United States, And the situation is particularly dire in rural and underserved parts of the Nation.  Add to this the fact that funding for community resources such as inpatient psychiatric beds and long-term behavioral health facilities has been shrinking for decades and it is not hard to imagine why the issue of access has become problematic for many who are in urgent need of psychiatric attention.

# 2. Because of stigma and denial surrounding mental illness, patients who most need care don’t always seek it

Stigma can be societal and manifest as discrimination towards people with mental health problems. A response from one of the other parents interviewed by Pelley, says it all: When Pelley asked her what the difference between being the mother of a child who has mental illness and the mother of a child who might have heart disease or cancer was, she answered with one word. Sympathy. Predisposing factors such as patient race, age, and health beliefs also influence an individual’s decision to access mental healthcare. Specifically, in the case of those living with serious mental illness, it is not uncommon for the patient to deny that he/she is ill and, therefore, think that they do not need help or medical treatment, i.e. they choose not to access mental healthcare. This denial brings with it a layer of complexity to interactions between mental health professionals and the patients they serve for, unlike many other illnesses, our patients may hide or not fully disclose essential aspects of his/her symptoms for fear of the consequences of such disclosures.

Another layer of complication is that federal and state laws, surrounding the involuntary hospitalization of individuals with mental illness, whilst designed to protect patient’s rights, often leave loved ones and mental health professionals who understand the patient and their illness with no voice, and minimal sway and influence over decisions that get made in courts. This situation emphasizes why it is so important that mental health professionals have the necessary time to carefully evaluate patients; be able to provide them with the continuity of care they need so that they can, eventually, develop a trusting relationship with their patient.  Often, it is through this trust that some aspects of denial can be challenged to ensure a better outcome for the patient. And this brings us to the next lesson

#3. Current insurance policies create barriers to patient access and encourage providers to offer reductionist mental health care services

The issues surrounding access to mental healthcare are further compounded by discriminatory, and often illegal, barriers to mental health and addiction services imposed by the health insurance industry. One of the most consistent debates that have raged in the psychiatric community, since the advent of managed care, has surrounded such insurance company policies and procedures.

Professional organizations have argued (successfully) that such policies appear to be designed to encourage psychiatrists to provide services that are reductionistic (as they are less time consuming and hence less expensive) and discourage approaches or treatments that: take more time; preserve continuity of care and build trust between patient and the professional caring for them. Americans with mental health disorders have been routinely discriminated against when they are required to pay higher copayments, allowed fewer doctor visits or days in the hospital, or made to pay higher deductibles than those that apply to other medical illnesses.

Whilst the signing of the 2008 Paul Wellstone and Pete Domenici Mental Health Parity Act has been viewed as breakthrough legislation to combat this discrimination it is important to note that the Act does not require employers to offer mental health or substance use disorder benefits, only that IF they are offered they must be offered on par with medical/surgical benefits. From 2014, under the Affordable Care Act, new individual and small group plans in and outside of the mandated insurances will be required to offer coverage. Barriers to the effective implementation of such requirements remain to be seen.

If a picture (in this case a 20 minute segment of TV news reporting) is worth a 1,000 words (in this case a 5,000 research or sober policy document) then this 60 minutes segment is that picture. I would encourage anyone with an interest in mental healthcare to watch it.

http://www.cbsnews.com/common/video/cbsnews_player.swf http://www.cbsnews.com/news/mentally-ill-youth-in-crisis/

ASAP Awards – Winners Announced

Earlier this month the six finalists for the ASAP awards were named. They represented six outstanding contributions to innovation that exploited Open Access. The 3 winners were announced at a kickoff event at the World Bank in Washington DC, on the Monday of Open Access Week 2013. This year’s OAW theme is “Redefining Impact” and few project speak more to that than the six finalists of the ASAP.

Nitika Pant Pai, Caroline Vadnais, Roni Deli-Houssein and Sushmita Shivkumar, developed a mobile phone app that will help people affected with HIV use a home diagnostic test and then connect with the right kind of information and the right kind of people. I asked Nitika about the project and about winning the award. Here is what she had to say:

Image courtesy of ASAP

The award inspires me to do more—and i thank God for rewarding hard work- and my family and my trainees for being there for me. I share this award with my extended family of trainees- Roni, Caroline and Sush who put in many hours of work with me. All of them pitched in, with their different perspectives. I am grateful to Open access— a movement that i strongly support, give my time and strongly believe in. i am an editorial board member of Plos one and review for Plos Med and several other open access journals.And i thank my sponsors—Google –and Wellcome Trust.

And finally, I dedicate this award to my husband, Dr Madhukar Pai, who is my role model. It was he who encouraged me to apply for it. As my future plans, lets keep our future plans for another interview. I do not like to talk about my work unless it is near completion…..i believe that our work and deeds should do the talking.

Read the full interview with Nitika Pant Pai here.

Mat Todd’s contribution to finding an open source solution for drugs to cure malaria speaks for itself. I talked to Mat about his project when he was named a finalist, and more recently I asked him about how he felt about winning the award:

Image courtesy of ASAP

Well, I’d want to emphasise:

I’m really happy to win this award. I am, however, representing a whole consortium of people. These guys have contributed because, I think, they just want to do the best science. They may have contributed because they realise we can do science more efficiently and with more impact if we’re open. The OSM-ers include people in my lab, in other labs around the world and the funders, the Medicines for Malaria Venture and the Aussie government, who had the courage to back a risky idea. Hopefully we can attract more people on board and do something extraordinary by discovering a drug that enters clinical trials.

Read the full interview with Mat Todd here.

Daniel Mietchen, Raphael Wimmer and Nils Dagsson Moskopp were nominated for the work they did “rescuing” multimedia files in  the Open Access literature. They built a bot that harvests these files and then gives them a new life in WikiMedia Commons. I’ve worked with Daniel and hope to work with him in the future, so I was really curious to ask Daniel what came next. Unsurprisingly, a lot. Daniel has so many great projects in his mind it is hard to keep up. The first line of his response was “Lots, actually” and here are some examples:

Image courtesy of ASAP

For instance, we could try to import media from other databases Dryad, Pangaea […], we could import files other than audio or video (e.g. images), or we could export to places other than Wikimedia Commons (e.g. YouTube).,[..] we’re not done, we’ve just tested the ground for bot-assisted large-scale reuse of openly licensed research materials, and we’d be delighted if others were to join in.

Plus, if we manage to reach out to the crowd (e.g. via the YouTube channel; then that could provide a new way for them to engage with scientific materials, and we can only imagine what people would do with them in a remix culture as on YouTube.

Read the full interview with Daniel Mietchen here.

Other finalists for the ASAP awards were:

Smartphone Becomes Microscope (Saber Iftekhar Khan, Eva Schmid, PhD and Oliver Hoeller, PhD)

Calculating Ecotourism Impact (Ralf Buckley, PhD, Guy Castley, PhD, Clare Morrison, PhD, Alexa Mossaz, Fernanda de Vasconcellos Pegas, Clay Alan Simpkins and Rochelle Steven):

Measuring and Understanding the Sea (Mark J. Costello, PhD)



ASAP Awards – Interview with Nitika Pant Pai

Communities with limited wealth suffer of diseases in a way that many of us may never come to be confronted with. Poverty befriends disease, and many diseases befriend shame.

Nitika Pant Tai knows this well and is dedicated to do something about it. She was one of the finalists of the ASAP awards for developing a phone app that will lower the barriers for HIV testing by removing the shame that usually comes with going to a clinic for the test. The phone app will help people do the test at home and connect with the right people and information.

Image courtesy of ASAP

I asked Nitika a few questions, and this is what she had to say:

Q. Can you tell me a bit more about the app?

NPT: I won the award for the HIV self -screening strategy and innovations developed for it. The app is part of that . The App is copyright protected and so we haven’t publicly released it yet.

It is an Android Google application (globally portable) that guides anyone who wishes to self test through the process of self-testing. Teaches them on what they need to know information on HIV, walks them through self test process (conduct and interpretation)  and linkages to clinics and counseling can also be operationalized with it. It works with an oral HIV self-test. Currently in English but will be translated into several languages and platforms.

Q: How closely have you been working with the target group for which you developed the app? What has their response or involvement been in the project?

NPT: For the past 12 years, I have conducted clinical research in HIV in marginalized populations worldwide (i.e., incarcerated populations in USA, STD clinic attendees and pregnant women in India, IDU’s and immigrants in Canada). I have also led and completed research projects in students and health care workers in Montreal and South Africa. So, I have been in touch with the needs of various populations in different contexts and settings.

To develop the application, we first started out with a paper application that we evaluated in different populations –formally as part of clinical studies and informally by introducing it to different groups- counselors, patients, providers for feedback. Then, we were funded by Grand Challenges Canada to conduct a study in South Africa. So we further refined our application- created an Internet application and tested content formally in a study in health care professionals. After doing that successfully, we converted it to a smartphone application and tested that for design, user interface, usability features. We are now trying to customize the application for various countries ( i.e., India, South Africa, Canada, to name a few)

I was thinking of s global self-tester when I thought of an app. I sought feedback from the HIV community – from patients, from my colleagues (HIV clinicians), from public health professionals, and from  people (that included members of my family-who are not into medicine, but familiar with apps). We showcased a first prototype at the London Self testing group, followed by GCC conference in Ottawa, and most recently at the International Aids Conference, in Kuala Lumpur. After a positive feedback , we decided to customize it for different settings and cultures for wider global applicability.

Q: How widely do you see this approach being adopted?

NPT: After showcasing it, I was convinced that there is a niche for it. I received requests from various groups (research groups, foundations, industry, and public health agencies)  so I do foresee it helping many people and I think it will be adopted by the digital savvy people.  We have different applications for different audiences.

Q: Going through your website, I found out that your focus is not just on HIV. What is it about those diseases that attracted your attention?

NPT: I have been involved in diagnostic research with point of care technologies for HIV and related co-infections (i.e., Hepatitis C, Hepatitis B, syphilis, TB) for about a decade now. I have focused on diagnostics and treatment issues around HIV. I had led Implementation research in both developed and developing settings.

Related diseases have attracted my attention, because often times, we fail to do a good job of diagnosing, treating or controlling HIV alone and people die from others (Hepatitis C, TB).  I have a passion for solutions to improve Women’s Health ( developing countries) and I am working extensively on that now.

Q: Do you think there is a potential to build similar apps for a broader range of diseases?

NPT: Of course! There is always an app to fill a gap! I have several now in my mind…wont spill the beans today 🙂

Q: How did you come to be involved in this line of work? Was there a trigger at some point that made you place your attention onto this line of work specifically, or was this just serendipity?

NPT: I am a trained medical doctor with a doctorate in research methods- and a masters in public health- my broad training helps understand all sides of the health spectrum. I realized early on in my career that treating patients can only go so far, and that my calling lay in treating and improving health systems- it didn’t happen like it happened for Gautama Buddha –under a tree– but certainly a lot of soul searching and introspection—deep introspection of your calling in life. And it happened at this magically transformational place called Berkeley, California. US offered me so many choices and wonderful people who served as great role models—so choices created confusion, but meditation helped zone in. This realization of my calling was fuelled and solidified when I enrolled into an MPH program at the University of California at Berkeley- It took me on a tangential track of academic research, a PHD in Epidemiology and Biostatistics and a deep interest in understanding the HIV epidemic –followed by a fellowship in infectious diseases and trials at McGill University, Canada. Several role models at Berkeley and San Francisco, Dr Jackie Tulsky, the late Warren Winkelstein, Art Reingold,  Jack Colford, Ira Tager were all physicians who changed their career tracks to public health and research inspired me. They supported me in plunging into my calling in life.  My husband, Dr Madhukar Pai was my constant support and role model and he encouraged and supported this radical shift from clinical surgery to public health.

After stepping out of my physician’s coat and all that comes with it—I began to listen to people– to patients, to front line health care workers, to staff. By listening to their woes, I realized I could help them by being their advocate. It wasn’t about what I wanted to prescribe them; it was about what they wanted to prescribe me for their betterment. That was a paradigm shift. It did teach me humility. I was way too arrogant before. I thought I fixed the clinical problem and that did it, sadly, it didn’t.

I continued with the line of research, when, I started out as a graduate student. I appreciated research  and now I teach clinical research methods to residents at McGill University and try to inspire them to think more…

The big picture issues of developing strategies for dysfunctional health systems that impacted several lives appeared more challenging and impactful to me, and fascinated me—I knew I could come up with solutions… Having seen them in close quarters in India.  After trying to understand US, Canadian and South African health systems, the functionalities, the ecosystem, and the dysfunctionality, (both the yin and the yang)  I thought harder about what I could do through implementation research and now, innovation.

I love working with people from all different backgrounds and I have a deep passion for the field of medicine and public health and love to solve these big problems that are complex, dysfunctional, complicated . I synergized all three.  Thankfully, my research got funded by Canadian Institutes for Health Research, and by the Gates Foundation. And innovations and challenging out of the box approaches got funded by Grand Challenges Canada, so these propelled me in the right direction. I conducted experiments in different settings: India, US, Canada,- South Africa. Each country presented its problems and its health systems. but—the a common denominator that we create solutions for is a human life!

My current project is a natural extension of my decade long independent work on oral fluid diagnostics for HIV.  I evaluated the accuracy of this test in tough rural settings in India. I developed an innovative strategy with oral self tests for women in labor, performed a meta-analyses on accuracy of these tests for self testing then moved on to evaluating self testing strategies. Armed by solid evidence, and training in methods and clinical disciplines, I designed strategies.  One thing led to another.  And then Grand challenges Canada happened. It sparked the innovator geek in me.  I wanted to do something different, and with GCC funding and support for out of box approaches, I pursued it. Solidified by evidence that I collected myself—after having convinced myself—I went ahead with that conviction.

I listen to no one but myself—very stubborn– you would say.  Even if I am in the wrong—I learn by making my own mistakes. My parents have always let me be-a philosophy that I carry on with my students, trainees and my own child. And I believe in old world values of universal good and cross cutting solutions that impact all people across the world.  I believe in Karma and destiny.  I am a visionary and a right brain dominant physician scientist, I imagine solutions of the future. I also love painting and cooking and writing poetry, my right brain balances my  analytical left brain.

Q: Would you like to say anything about the broader topic of being a woman in this line of work, or about how your ethnic identity/history influences the way you go about your career or ow others may perceive you because of that?

This is one of my favorite topics. I think it is a chapter in itself.:-)

In Canada, there are many women in medicine and science. So, I don’t face any gender bias on a daily basis. But when I travel and work in other cultures, there are few women, then I do. So you do face egos and have to keep reacting to that in check. Sometimes, you need to dissolve your own ego  to understand where sexist opinions come from.

Women in my line of work need to believe that they can do justice to themselves and to their careers—they need to be grounded and be tuned in to their own needs as well as to the needs of their families. Often times their days and months wont be perfect, their homes wont be perfect, they would feel totally exhausted, but they need to give in to that imperfection to enjoy their lives.  We women learn to Juggle—but learn to switch off- for your families—for yourself—because no one dies for work–

I am a strong feminist—I grew up in an overtly gender biased society in India, before I moved to North America, where I experienced another form of bias—of being perceived as different (ethnically different). Thankfully I moved around in an academic circle, where people are exposed to other cultures and are more forgiving, so they didn’t make me feel like the odd one out. But you have to learn to ignore that uncomfortable bit!

I believed all along that men and women were equal. Women are naturally talented, but because of centuries of suppression in other cultures, and negative self talk, self esteem issues,  and pain body as a consequence—they oftentimes give up!—even before running the race… sometimes they seek satisfaction elsewhere- I am happy to be in an environment at McGill where 50-60% of our divisional faculty are women. Strong women with strong careers and families who have inspired me that it is possible to have both….. and you have to juggle to do what makes you happy.

McGill University also embraces diversity and provides a great environment to work in for people from other cultures. So I love working there. I inspire other women now- some of my trainees suggest I become a motivational speaker or coach for them. 🙂

I believe that everyone on this planet is equal regardless of their DNA or the color of their skin or their background. I come from a family of educated professionals (lawyers, administrators, healers) a family with about 2-3 generations of educated men/women. And thankfully, progressive fathers and grandfathers, who believed in gender equality, so the confidence in  myself as a woman stems from it. My parents (both my mom and dad) raised me with a strong value system of honesty, integrity and hard work. So I never doubted my capacity —but I had to be careful in a overtly gender biased society in India and in a different society in North America, where I am perceived to be different.

If people treated you differently, it was a problem of perception.  It is easier to think of an immigrant stereotype-—and I understand that. But you know US and Canada are built of and with immigrants—the term being an immigrant is relative, and is a function of time when you arrived—sometimes that varies in years, or, sometimes in centuries. But for the immigrant hard working work ethic, and strong values, they would not be a land of choices and opportunity.  So it is all about our mindset and how we view the world. And in today’s day and age, the world is very small!! People from America live and work In Asia. The boundaries are more blurred.

As for myself, I continue with my work—ignored the perception—:-)

ASAP awards – Interview with Mark Costello

ASAP Finalist Announcement 600x600Mark Costello, a researcher at the Institute of Marine Science and Leigh Marine Laboratory (University of Auckland in New Zealand) was nominated for his work with WoRMS of which he was founding chair. The site provides a database of scientific names for all marine species. Species are sometimes described with different scientific names, and the site helps disambiguate these names and also provides or links to information about each species.

Q: How did the project come about

Courtesy of ASAP awards

MC: When I was in Ireland 1990’s I was involved in workshops developing policies for biodiversity – the main barrier was lack of coordination of species names. This meant we couldn’t merge datasets easily enough. In 1996 I put in a proposal to create an inventory of science species names which was funded by the European Commission. Since 2004, the Flemish Government has funded the hosting of the database. Once the infrastructure was secure and professionally managed, then getting the info into it became possible. People were motivated because this was a permanent website with permanent support from the Flanders Marine Institute (VLIZ). It started as a clean-up exercise.

Q: What is special about the site?

MC: By providing naming information about species, it helps people navigate the scientific literature where alternative names may be used, but it also links to information about the species.

Q: What did you learn from working on WoRMS?

Courtesy of Mark Costello

MC: There were unexpected patterns that were discovered from the data. We discovered that the number of species being described over time has been increasing at a linear rate. When you look at the authors there are now about 3-5 times more people discovering species than ever before – so taxonomists are not really disappearing as many people have said. The number of species discovered per author is, however, declining. That it is taking more people to discover species than it did before suggests that we have discovered most species on Earth (at least half, perhaps 2/3), not only a small fraction as some have speculated. We found also that science is doing better, conservation is working.

Q: What was people’s response?

MC: Word of mouth helped – there was an element of trust. We only know the people we know – but when you look globally you start to get a different picture than when you look at your own community. The taxonomy is curated by specialists, and people are now more trusting about online collaboration than when we started. But it was important to have a long – term commitment to supporting these databases to make the system sustainable so that the databases are shareable.

According to their stats page, In 2007 the site had received 37,221 unique visitors and by 2012 this number had risen to 817,335 unique visitors and 30,423,583 page views. The material is provided under a CC-BY, although permission needs to be sought for the re-distribution of the entire database, and it seems too to download the entire database too. I asked Mark about that.

MC: I don’t think that the CC-BY is a hindrance for sharing the data or reusing. We provide a clear citation for the data. We want the source to be cited because we consider it a scholarly publication. And users concerned about quality assurance of their sources can then cite it as an ‘authoritative’ rather than anonymous resource. When you combine the data into a new set, people that want to use this new group or want to replicate need to know where the original data came from. Otherwise they would be having to start from scratch. The citation solves this problem.

Courtesy of Mark Costello

MC: The request was put there originally because databases change over time and we were worried that there would be multiple copies which could create confusion as to what is the best source. It also was a way of not having to deal with data flow issues if too many people were downloading the entire database at the same time. We also needed safeguarding from attacks of sending constant queries to the database. But it is also a good way of knowing and tracking who your users are, so we can provide the list of organisations that use the database when we are out looking for funding and support.

Q: What would you like to see next?

MC: I would love to have all species on Earth in a quality approved database and see what we could then discover about the species. We learned a lot from querying this database, and we could learn a lot more if we had all species in there.

Even if you are not interested in digging into the data, the site is a great place to get to know our underwater neighbours. I encourage you to visit the site.

ASAP awards – Interview with Daniel Mietchen

ASAP Finalist Announcement 600x600 The names of the six finalists for the ASAP awards are now out, and I was pleased to see Daniel Mietchen’s name in the list. Daniel Mietchen, Raphael Wimmer and Nils Dagsson Moskopp have been working on a really valuable project. There was an opportunity in exploiting open access literature to illustrate articles in Wikipedia.

Courtesy of ASAP awards


Many scientific articles have a “supplementary” materials section, which can be rich in multimedia, but these artifacts may not as easy to find as those that make up the main body of scientific manuscripts. What Daniel, Raphael and Nils did is maximise the impact of those research outputs by putting them in a place where they can be found, explored and reused by scientists and non-scientists alike.

They developed a tool called Open Access Media Importer (OAMI) that searches for multimedia files through Open Access articles in PubMed Central and uploads them to WIkimedia. This tool exemplifies the added value of papers published under open access using a libre copyright licence such as CC-BY. Not only are the articles available to read, but also they can be repurposed in other contexts. The files that the OAMI bot uploaded now illustrate more than 200 English Wikipedia pages, and many more in other languages.

CC0- Uploads by OAMI bot to Wikimedia Commons between 7/12 and 9/13

Q: How did you get started with this project?

DM: My PhD was on Magnetic Resonance Imaging, which primed me to work with videos, and my first postdoc was on music perception, which naturally involved a lot of audio. Both made me aware of all the audiovisual material that was hidden in the supplements of scholarly articles, and I found that the exposure of that part of the literature left much to be desired. For instance, every video site on the Web provides thumbnails or other forms of preview of video content, but back then, no scholarly publisher exposed video content this way. Wikimedia Commons did. I also noticed that Wikipedia articles on scientific topics were rarely illustrated with multimedia. So the two fit well together. Nils, Raphael and I met online, and then sent our first funding proposal in 2011 in order to automate the import of supplementary audio and video files from scholarly articles into Wikimedia Commons.

Q: How did you get started with the project?

DM: We chose to start with PubMed Central. It is one of the largest repositories of scholarly publications, many of which have supplementary materials, and it has an API we could use.

Q: How far have you come?

DM: We have now imported basically all audio and video materials from suitably licensed articles available from PubMed, save a few where there were technical difficulties with file conversion or upload. Initially, we did not know how many files this would be, and had roughly estimated (there is no easy way to search for supplementary video or audio files) the number at somewhere between 5,000 and 10,000 back in 2011. The bot now adds several hundred files from newly published articles every month and passed 14,000 uploads to Wikimedia Commons earlier this week. So if you are going to publish multimedia with a suitably licensed paper in a journal indexed in PubMed Central, you – and anyone else – can find it on Commons shortly thereafter.

Q: How does that compare to other Wikimedia content?

DM: Most of the uploaded files are videos, and given that there are about 36,000 video files on Commons in total, about one third of them now has scientific content. That is a much higher proportion than, say, that of scientific articles out of all articles on any Wikipedia. However, the number would be even higher if more authors (or journals) would decide (or funders mandate) to put their materials under a Wikimedia-compatible license. If materials from their papers cannot be reused on Wikimedia Commons, they are not Open Access.

Q: Were there any hurdles along the way?

DM: Sure. The project actually evolved more slowly than we had anticipated because we had underestimated the extent to which the standards for machine readability of manuscripts deposited in PubMed Central are being ignored by publishers, or interpreted in a rather inconsistent fashion. We put forward a number of suggestions to PubMed Central – who are very cooperative – in order to monitor standard compliance and to facilitate reuse by us and others, and we’ll present a paper on that at a conference during Open Access Week.

Q: What else can OAMI do, and how can people have access to it?

DM: The software is available on GitHub and was built to be both reusable and extendable, so if someone wants to write a plugin to export the videos from PubMed Central to places like YouTube, they can start doing that right now (in fact, work on a YouTube pipeline has already started). Or we could think about harvesting in places other than PMC, or materials other than audiovisuals. If anyone has ideas in this regard, they would be most welcome.

Q: What comes next for you?

DM: This was and is a spare time project and will likely continue as such for some time. While it was a perfect fit to my Wikimedian in Residence project at the Open Knowledge Foundation Germany that ended this summer, I am continuing to work at the interface between research, openness and the public, as I am now at the Natural History Museum in Berlin, working on the pro iBiosphere project that aims to lay the ground for integrating biodiversity research with the Web, which will require a greater degree of openness than what we are used to now, as well as better machine readability of the relevant information, a topic that I am currently focusing on.

I met Daniel online a few years ago, and he has been a source of motivation and inspiration for a lot of us. It makes me very happy to see that his work has not gone unnoticed, and look forward to seeing the outcome of his next projects.

ASAP awards – Interview with Mat Todd

ASAP Finalist Announcement 600x600
The name of the six finalists for the ASAP awards are out.

Backed by major sponsors like Google, PLOS and the Wellcome Trust, and a number of other organisations, this award seeks to “build awareness and encourage the use of scientific research — published through Open Access — in transformative ways.”

One of the finalists is Mat Todd for his participation in the Global Collaboration to Fight Malaria.

Few research projects reflect this spirit of Open Science as well as the Open Source Malaria Project which is trying to find molecules that can help fight this terrible disease. Unlike other drug discovery projects, they are building on compounds that have been put the public domain and making the discovery process not only open for anyone to look at but also for anyone who wants to participate to do so – whatever that contribution might be.

Courtesy of ASAP awards

I had a chance to talk to Mat Todd the other night and he was gracious to answer some of my questions.

Q: What made you get engaged in Open Research?

MT: I kept looking around me and finding problems that were not being solved efficiently because people are not exploiting the power of the Internet to work together. Putting your work on the web helps to get greater interaction and find the best people to work with you. The psychological barrier, however, is that in the process you lose control of your project and failures are clearly revealed.

Q; How do you get people to overcome those barriers?

MT: I don’t know.  You need to have the attitude that something needs to be done and done really well, even if it is not ultimately done by you. We should assume that the next generation will adopt approaches to solving problems that are more fluid than how they are today.

Q: How did the Open Source Malaria project get started?

MT: We built on an earlier project that solved how to make a drug in an improved way, something that was needed by the World Health Organisation. (here and here) We thought “how about extending this to drug discovery?” That’s interesting because there you have the issue of whether you need patent protection, which is seemingly at odds with a totally open approach. We were able to start with data that GSK had put in the public domain in 2010. This move by GSK was pretty incredible, but they had so many compounds that were active against malaria that they considered putting the data into the public domain as a sound idea to increase their interactions with other scientists. Open data stimulates research activity by others.

Q: What do you think this project means to the Open Science movement?

MT: The project lets people see the process and that might get people more interested in what science is: there’s nothing mysterious about it, just people doing work. The Open Source Malaria project also eschews patents, and that means you need to think about whether new medicines can be taken all the way through to the public without that kind of protection – that’s actually what the session I’m running at OKCon at the moment is all about. How will we cover downstream costs of making the project’s discoveries available to people? Generally though, there is a fair amount of pressure on the project – we need to get it right because we don’t want the project to become the example of open science not working!

Q: Do you think this open source model can be exploited for other diseases?

MT: Diseases vary in their risk and complexity, so it will depend on the disease. Phase III clinical trials is typically the cripplingly expensive bit and drugs can often fail there after lots of investment. In the case of malaria the full set of clinical trials may not be so costly. There is something to be said for the open approach de-risking the whole process because you ought to be more confident in the quality of the drugs you’re trialling. I think the answer to your question is “yes” in short. More generally though we need to think beyond financial profit and start thinking that healthy people are more productive – that changes the reasons why public funds might be used to cover these huge costs.

Q: Where is the project at?

MT: We have been focusing on the data and getting the project going, so we have not rushed to get the paper out. The paper is crucial but it is not the all and all. The process has been reversed, we first share the data and all the details of the project as it’s going, then when we have finished the project we move to publishing. The project itself has just started looking at a new series of very nice compounds that have also come from the private sector and have been put in the public domain by MMV.

Q: What have you come to enjoy about participating in the project?

MT: What I love about it is working with really smart people wherever they are, from students to professors, Australia through Europe to the US.

 Q: And where do you think Open Science is at?

MT: Very early days. If everyone in the world did open science then it would just be science and I could stop talking about it…

I came across Mat online several years ago, and he, like most others that participated in the Open Science discussions, helped shape my thinking and strengthen my commitment to a better way of doing science. We talked a bit about those “good old days”, and he ended the conversation with a quote from Charles Dickens:

“We are all sailing away to the sea, and have a pleasure in thinking of the river we are upon, when it was very narrow and little.” (From Dickens, C. (2012). The Selected Letters of Charles Dickens. Oxford University Press)