People power … crowdsourcing for science

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I am a keen albeit largely unknowing participant in crowdsourcing. I do it almost every day, many times a day. It seems I just can’t get enough. And you are probably the same.  Of course I am alluding to the use of search engines, particularly useful when attempting to glean some degree of understanding from almost incomprehensible journal articles. While you are happily tapping away flitting from site to site, your movements are tracked and fed back to ‘X’ within a process called data-mining; information which can be used to
to modify existing systems, such as online ad. words. In essence you are ‘involuntarily’ contributing to crowdsourcing.  But perhaps this is not such a good example, as I think the concept of crowdsourcing has developed much more positive connotations than it possibly had when the phrase was first coined. So let’s rewind a little….

Crowd + Outsourcing = Crowdsourcing

‘Crowdsourcing is the act of taking a job traditionally performed by a designated agent (usually an employee) and outsourcing it to an undefined, generally large group of people in the form of an open call.’  Jeff Howe

(http://www.crowdsourcing.com/)

Crowdsourcing is certainly not a new phenomena eventhough the term was only coined in a 2005 online article by Wired Magazine editor, Jeff Howe. One of the best known historical examples is the development and compilation of the Oxford English Dictionary. An open call was made to the public for contributions to identify all the words in the English language, and ‘provide example quotations of their usages for each one’. Over a period of 70 years over 6 million submissions were received! While this involved pen, paper and postage stamps most crowdsourcing today is initiated and conducted using the internet as the key information-sharing medium.

More contemporaneously in 2009 Iceland turned to crowdsourcing amongst its citizenry to write a new constitution.  http://www.opendemocracy.net/can-europe-make-it/thorvaldur-gylfason/democracy-on-ice-post-mortem-of-icelandic-constitution

And the internet itself largely remains relevant from crowdsourcing as millions of people contribute content. Wikipedia, from where I sourced the example of the Oxford English Dictionary, is the poster child for this form of crowdsourcing – ‘wisdom of the crowd’ –  but which is not without its flaws. I had not known until very recently (when I finally bothered to google it) the term ‘wiki’ literally means, ‘A Web site developed collaboratively by a community of users, allowing any user to add and edit content’…. IE Crowdsourcing!

One of the key ideas behind crowdsourcing is simply inviting the more people to work on a project or problem will lead to more rapid and creative outcomes – and usually cheaper if not free.

Crowdsourcing is also providing exciting opportunities for the science community to tap into the time, intellect and funding of the greater public. In this context crowdsourcing can be known as Citizen Science. A direct form of science crowdsourcing is data collection in the field. A local example is the Atlas of Living Australia .

Community organiser and contributor Libby Hepburn reflected, ‘technology has come to the point where the public can get involved in science. With your digital camera, you can make a valid record, which a scientist can then confirm. And by getting the public involved, we’re covering far more than scientists could do on their own.‘ (https://open.abc.net.au/posts/crowdsourcing-for-science-52fs5py)

For Science researchers, crowdsourcing can also involve outsourcing hundreds of hours of data processing saving them time and money and producing multiple unique scientific results which may range from ‘accidental’ individual discoveries to ‘those using classifications that depend on the input of everyone who’s visited the site’ . Major crowdsourcing proponent, Zooniverse (www.zooniverse.org) calls it ‘serendipitous discovery’, which is explained as a ‘natural consequence of exposing data to large numbers of users, and is something that is very difficult to program into automatic routines’. This is in contrast to the scenario of ‘distributed computing’ where a volunteer doesn’t have to do anything but let their computers run data when it would normally be idle.

I am interested in the potential of the crowd to brainstorm ideas; either to solve a particular problem or to identify subjects for research which I see as another key form of ‘community’ building (within and without the Science research field), sharing knowledge, experience and judgement. One example I came across invited readers to ‘Think of this post as an experiment in open review of a pre-experiment hypothesis. Keen to hear your thoughts!’ in seeking input/feedback about a research proposal.

A creative and wildly popular example of successful crowdsourcing for scientific research was developed by the University of Washington’s Center for Game Science with the Department of Biochemistry. The online community was invited to play Foldit; an ‘online puzzle video game’ about protein folding. It is a bit longwinded to explain properly and so I have attached a brief video from one of the creators, Adrien Treuille. The game creators, however, were fascinated to see the online conttributors sharing experience and learning together to improve outcomes (game results) which eventually resulted in the worst human-contributed result being better than the best computer generated contribution.

  (5min)

(A more detailed analysis of the project presented by Adrien Treuille, called ‘Crowdsourcing science: 10 reasons to crowdsource science’ can be found on youtube  http://www.youtube.com/watch?v=Ia2qBqfZROE&feature=player_detailpage  Duration: 1hr)

Crowdsourcing as Citizen Science

Crowdsourcing can also be seen as a significant tool to opening up science to the general public, albeit mainly online, and in many cases actively engaging them in projects as contributors. Under the umbrella of citizen science, the University of South Australia’s Barbara Hardy Institute under the branding of ‘Citizen Science’ has utilised the public capacity to collect data in the field for several major projects including the ‘2012 Great Koala Count’, and ‘Bring us your bugs’.

‘Citizen science is a research methodology where scientists partner with the public to conduct scientific research.’

(https://www.unisa.edu.au/Research/Barbara-Hardy-Institute/Key-Research-Projects/Creating-Biophilic-Cities-through-Citizen-Science/)

This form of crowdsourcing is also about developing positive relationships between the scientists (and university) and the public and key to this is conferring a sense of ownership of the research to the community. Importantly this type of outreach work while also serving an important research purpose engages a great variety of people and is particularly accessible and appealing to children. The university project group observe, “Citizen Science involves the participation of the wider community (particularly non-scientists) in scientific projects. Proponents of Citizen Science, when listing its benefits, usually begin with how it enables extensive data collection. Indeed, this benefit is considerable; but it is the interaction between scientists and the community, and the ability for projects to inform both groups, that are perhaps the most exciting outcomes of this approach.”

Zooniverse: ‘While the primary goal of our projects is to produce academic research, by their very nature they are also outreach projects. As it involves our volunteers directly in the process of research, citizen science is a powerful tool for both formal and informal education.’  (https://www.zooniverse.org/researchers)

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Sketchnote by Perrin Ireland from ScienceOnline 2012

Crowdfunding:

A promising off-shoot of crowdsourcing is crowdfunding and probably something which one wouldn’t think could be transferred to science but it has although initially only for smaller projects. Crowdfunding entails putting out an open call for research funding and there are now many websites which act as mediators between the researcher and potential funders, such as scifundchallenge.com,   Other researchers have gone straight to the public like ?   Overall, the results have been positive for smaller

projects, particularly in light of the difficulty many researchers have to secure even minor amounts of funding which can be all important to complete research and have the results published – critical to a career in research.

An interview by ‘Masala Skeptic’ (posted on skepchick.org late last year) entitled ‘Crowdsourcing Science’ featured collaborating research scientists setting out to find crowdsourced funding for their research project. The interview provides some interesting insight into the potential as well as the practicalities of this approach.

Interviewee and biotechnology researcher Ethan Pearlman expresses a common perception:

‘The system of funding science right now needs an overhaul. We are still using archaic and inefficient methods to fund basic research. Last year, only about twenty percent of all grants that were submitted to the NIH (National Institute of Health) and to the NSF (National Science Foundation) were awarded… We went with a crowd funding approach because it leads to direct interaction between the general public and scientists conducting research in real-time. We want all of the aspects of scientific research to be readily accessible to the general public. That includes the finances… By funding our research, people are becoming invested directly in the science. They start caring about the project. I hope that this will translate to a more general curiosity about science.

This is not an uncommon sentiment and crowdfunding certainly provides a refreshing alternative to traditional funding sources for research scientists but I wonder given the sense of ‘moral’ accountability to independent contributors, is this funding model a greater or lesser burden? More or less independence from the funding source? More information about Ethan’s project and crowdfunding endeavours can be found here on a crowdfunding portal rockethub.com.

However…

In his blog post, ‘The Limits of Crowdsourcing in the Scientific Disciplines’, Senior Editor with Oxford University Press and former research scientist David Crotty sees crowdsourcing as manifesting inherent conflicts between egalitarianism and expertise. He doesn’t believe Science can be outsourced as it requires specialist training, experience and expertise – therefore precluding it from being egalitarian. I think what he means is the pursuit of scientific discovery and its process should not be the result of a popularity contest…. although heading in the other direction where the premise is ‘scientists know best’ also leads us to questions of accountability for how taxpayer funding is applied in the best interests of the community – and who should determine that?

The particular bee in Crotty’s bonnet relates to public review of papers for publication. Crowdsourcing reviewers has some inherent problems. Traditionally we have relied upon experts for peer review to assess and legitimise (or not) the quality of the work undertaken. This is the designated quality control. Crotty somewhat facetiously enquires whether we should instead turn to crowdsourcing to determine if a paper is accurate, meaningful and useful through a popularity vote. As he phrases it, ‘Should a bottom-up approach replace the top-down system in place?’ He has a point where online statistics reflect whether a piece is ‘liked’ or cited (which may be as a result of it being accessible) rather than assessing if it has scientific merit. The ….and vulnerable to biases and directed manipulation.

But is Crotty just protecting his income stream against free access journals? He chooses not to acknowledge the long-standing inequity which crowdsourcing and open source models seek to address. Are his arguments, while containing several valid concerns, just as much about the (re)democratization of science?

I do, however, agree with his concluding statement which we would do well to remember to avoid getting carried away,

Social approaches can offer enormous value, but they must occur in the right context for the results offered. It may not seem fair to everyone, but not everything in this world should be put to a vote — even if we have the technology to make it so.’

Understanding why people choose to participate/contribute to the less engaging and interactive forms of crowdsourcing would be interesting. For some people it is about income while others participate as a social experience and the personal reward of connecting or contributing. Can it be purely altruistic? Do people just wnat to belong to something (or anything)? Is it a real albeit small way of making a mark? Perhaps largely vicarious?

Whatever the reasons, crowdsourcing is a dynamic and exciting social movement with much potential as a tool serving scientific research and outreach to facilitate a democratization of science (open science). If you are interested in hearing more about crowdsourcing and open science check out this video featuring Australian Micahel Nielsen – an academic, Tedtalk presenter and international advocate of open science.

Until next time. DS

 

(If you like the work of musician Gotye, here is an crowdsourced remix of his song, ‘Somebody that I used to know’, called “Somebodies: A YouTube Orchestra.”)

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A Fatal Attraction to Fungi in 8 Graphics

As a Thursday night post I’ve decided to share my mini class presentation with you. How lucky are you?! (But ‘lady luck’ could be a whole other blog post topic…)’

As part of the assessment for our ‘Communicating with Science’ course we were required to mentally digest and communicate the contents of a peer-reviewed scientific journal article in a 2 minute timeslot followed by a brief Q & A with our classmates and a couple of obliging ring-ins. It was a very useful and practical exercise pin-pointing what the most significant and interesting aspects of the paper were with a view to being able to then communicate the information clearly and accurately… and of course, engagingly. With another assignment due the previous night preparation time was limited…

I opted for a 2013 paper I had already read for my blog post, ‘Why might stinky feet be so important in the fight against malaria?’ but had only briefly referenced. This is a tale of fatal attraction and I hoped its quirkiness might appeal to the audience comprised of my classmates (and assessors) as it had to me.

The Paper…

George, J, Jenkins, NE, Blanford, S, Thomas, MB & Baker, TC (2013) ‘Malaria Mosquitoes Attracted by Fatal Fungus’, PLoS ONE , vol. 8, no.5.

The paper detailed experiments focussing upon fungus as an active ingredient in a biopesticide control of malaria mosquitoes. I love it when the natural world has the answers, and especially when those solutions can trump our own ‘inventions’ and their associated adverse side effects. And so the concept of biopesticides (with a likelihood of less harmful side effects) seems really cool to me.

The Presentation…

Slide 1.

Malaria is a mosquito-borne infectious disease. It begins with a bite from an infected female mosquito, which introduces the microorganisms through saliva into the circulatory system from where they travel to the liver to mature and reproduce.

A mounting problem with preventative measures for controlling malaria is that mosquitoes are becoming resistant to some chemical insecticides and so some researchers are looking at alternative biopesticides (‘a form of pesticide based on micro-organisms or natural products’).

(Click on slide for enlarged image)

Slide1

Slide 2. 

In this case the active ingredient under research is a fungus called Beauveria bassiana which infects insects and kills them slowly (in relative terms for insects… 1-2 weeks for mosquitoes).

(Click on slide for enlarged image)

Slide2

Slide 3. 

Previous research has shown insects may be deterred from landing upon pesticides which are harmful to them. If the fungus proved a deterrant to its target than it would not be an effective active ingredient in a biopesticide. Hence, the researchers wanted to see if mosquitoes would be repelled by the Beauveria bassiana. They did this by giving a ‘cage’ of mosquitoes a choice between two fungi using a y-tube olfactometer (I like to call it a ‘smellometer’). And to the researchers’ collective delight, the mosquitoes chose Beauvaria (despite its fatal effects) over the less harmful and obviously less sweeter smelling Penicillium. This suggested the Beauveria bassiana smells almost irresistible to female mosquitoes. That would seem to suggest the researchers had been successful in reaching the objective of their experiments… but they wanted to go further. They knew mosquitoes would almost definitely become infected by landing upon a surface to which dry fungi spores had been applied (tests showed a 95% likelihood) but this would likely prove a very onerous, time intensive and expensive task – especially when considering the extent of land where malaria is present. And so the researchers also looked to prove that Beauveria bassiana is irresistible to female mosquitoes through ‘natural’ transfer.  

(Click on slide for enlarged image)

Slide3

Slide 4.

In this case, the fungus takes advantage of the mosquitoes somewhat gruesome predilection for feeding upon insect larvae, dead or alive. And mosquitoes are particularly partial to the squishy, tender bodies of caterpillars…

(Click on slide for enlarged image)

Slide4

Slide 5.

… which may already be infected by Beauveria bassiana and dying a slow death. The researchers tested a hypothesis that female mosquitoes would be drawn to infected caterpillars over infection free caterpillars. (Click on slide for enlarged image)

Slide5

Slide 6.

The earlier test was repeated but with cadavers of caterpillars infected with Beauvaria bassiana against caterpillar cadavers which weren’t infected. Similar results were achieved.

(Click on slide for enlarged image)

Slide6

Slide 7.

While this proves that Beauveria bassiana could be a very useful active ingredient in bio-pesticides to prevent malaria, the researchers couldn’t fully explain the fatal attraction the fungus had for the female mosquitoes. These are also experiments at the early stage of developing a biopesticide. Conclusion: More research needs to be undertaken.  

(Click on slide for enlarged image)

Slide7

Slide 8.

Interestingly, research has also shown, the slow death by biopesticides (in comparison to the rapid death caused by insecticides) also makes it harder for the mosquito population to build up a resistance. Isn’t that cool considering the ability of mosquitoes to build up resistance to traditional pesticides has been affecting the ability to control mosquito populations recently? Win-win, I say.

(Click on slide for enlarged image)

Slide8

In case, you’re wondering – Yes it did run over the allocated two minutes…. do you know how fast two minute speeds by? Feedback suggested I could have left out slides 4, 5 & 6 and just covered the key investigation of the experiment.

Interesting questions I fielded from the audience included among others: whether application costs of biopesticides were affordable and would this affect its viability ergo was cost a factor between traditional pesticides and biopesticides; and could mosquitoes infect eachother… do they feed on eachother as they do on other insects? Do any readers know the answers?


Why might stinky feet be so important in the fight against malaria?

Not so long ago while flicking channels as is my usual bad habit I caught part of Tony Jones’ interview with Bill Gates on a special feature episode of ABC television’s Q and A during Gates’ fly-in-fly-out visit to Australia promoting the Bill and Melinda Gates Foundation. I was curious for as founder of Microsoft he doesn’t have a particularly positive image among more liberal (note the small ‘l’) thinkers. And apart from the negative press I knew little about him or the foundation. Well, I may be gullible but I was quickly impressed by his quiet manner and the way he spoke in a fairly self-deprecating style.  Furthermore, my long-held sympathies towards developing nations struggling with diseases which we are hardly aware of in Australia were touched by the sincere and intelligent response from Bill Gates to a question from a Papua New Guinean Health worker.  I am including a clip below if you are interested in hearing what he had to say.

 

Since then I have been doing a little reading about malaria and the latest reported research (across disciplines). From a simple web search one quickly sees there are a great many groups working towards reducing the incidence of malaria around the world through preventative measures such as supplying mosquito nets, removing mosquito ‘habitat’ or implementing vaccination programs, research, community development, health education, and there are also a great many people supporting through donations and fundraising. Recently, two young university students from Burkina Faso and Burundi won the Global Social Venture Competition (GSVC) for inventing a mosquito deterring soap which they named Fasoap. Quoted in an online article they said, “In our country the majority of the population lives below the poverty line… most people can’t afford to regularly buy medicines and products such as anti-mosquito creams, sprays or protective nets,” but Fasoap will be cheap enough for most households to afford to use and can replace the standard soap in the house.

Soap Creators, Moctar Dembele from Burkina Faso and Gerard Niyondiko from Burundi

Soap Creators, Moctar Dembele from Burkina Faso and Gerard Niyondiko from Burundi

Malaria is a mosquito-borne infectious disease. It begins with a bite from an infected female mosquito, which introduces the microorganisms through saliva into the circulatory system from where they travel to the liver to mature and reproduce. Symptoms of malaria may include headache and fever and can lead to coma and/or death. Unfortunately there is no vaccine yet. Resistance has already developed to several anti-malarial drugs and increasing resistance to others is becoming a problem. (Thanks to Wikipedia for some of that info). Malaria is a huge problem affecting thousands of people through ill-health as well as the loss of loved ones. The loss of economic productivity for families, communities and developing nations is also immense and an obstacle to poverty alleviation and sustainable development in many affected nations.

A novel area of research is looking at the use of insect-killing fungus such as Beauveria bassiana as an active ingredient in biopesticides (‘a form of pesticide based on micro-organisms or natural products’[i]) against mosquitoes which transmit malaria. This has become necessary as mosquitoes become increasingly resistant to existing to conventional chemical insecticides. Interestingly, research has also shown, that the slow death by biopesticides makes it harder for the mosquito to build up a resistance.

Malaria kills more than 600,000 children each year and although this seems amazingly high there is only a mortality rate of 0.3% reflecting the high number of reported cases of over 200 million. Early diagnosis and treatment significantly control the mortality rates but it has also been proven that some people (particularly from regions in Africa) are naturally able to resist greater severity of the disease suggesting genetic factors play an important role.

Current research is looking to identify the genes affecting an individual’s immunity to malaria and from this potentially understand the molecular basis of protective immunity against the disease – and be able to apply this to the development of an effective malaria vaccine. For example researchers from MalariaGEN (Malaria Genomic Epidemiology Network)[ii] are conducting four key areas of research addressing different aspects of the problem:

  • Genetic determinants of resistance to malaria
  • Genetic determinants of the immune response to malaria
  • Human genome variation in malaria-endemic regions
  • Genetic linkage studies of resistance to malaria

The following animation from the Wellcome Trust Centre for Human Genetics (Oxford, UK) which is ‘home’ to MalariaGEN cleverly explains the purpose of the research. It also has a good percussion soundtrack so turn on your audio.

This is all interesting reading for some but all of you (whoever you are) may also be wondering where smelly feet come into it or if that was just a ruse to lure you into reading my post. Well you are half right – it was designed to lure you in but it isn’t a ruse.  I was inspired by the recently published research (peer-reviewed), ‘Malaria Infected Mosquitoes Express Enhanced Attraction to Human Odor’[iii], and some associated reporting[iv].

There is existing evidence some pathogens (such as malaria) can manipulate their hosts or the vector (the mosquito) to better aid in their spread from their mosquito host to assist transmission. The researchers, Smallegange et al (2013), have found mosquitoes are more likely to be attracted to human odour than others and malaria-carrying female mosquitoes (Anopheles gambiae sensu strict) are even more attracted to the human odour than those that are not infected. This is better illustrated by the useful little graph below sourced from the published paper.

Attraction of malaria infected mosquitoes to human odor. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0063602

Attraction of malaria infected mosquitoes to human odor. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0063602

To cut a long story short Smallegange et al discovered this by using a nylon matrix which had been treated with human odour and a clean control nylon matrix placed in a cage olfactometer with 20 infected mosquitoes and proceeded to count how many times and beneath which nylon matrix the mosquitoes landed (including ‘probing attempts’) in a 3 minute period. The same test was separately undertaken with uninfected mosquitoes.

[As an aside, I can imagine you wondering what a ‘nylon matrix’ is – some wondrous piece of technologically advanced lab equipment? Perhaps some sort of synthetic (nylon) net (matrix)? As it turns out what they used was simply a ‘panty-sock’ – which I take to mean some version of pantyhose. And they acquired the human odour by availing a man to wear the said panty-sock for twenty hours prior to the experiment. For those who may have any concerns for the man providing foot odour, the lead researcher/author also ‘performed odour collection on herself by wearing nylon stockings’. (!?!?)]

The results show infected female mosquitoes are more attracted to human odour than non-infected mosquitoes, indicating the pathogen effects the mosquito host’s behaviour and most likely in within their olfactory system. There is further research to be done to determine what impact the lifecycle stage has on the host’s attraction to human odour, as well as odour from multiple human subjects.

Why is this important in the fight against malaria? The researchers point out, ‘Further studies on the identification of new attractants for improved mosquito surveillance or trapping programs specifically targeting P. falciparum infected An. gambiae s.s. [malaria carrying mosquitoes] females may provide powerful tools for the global agenda of malaria eradication’(p.3).  Furthermore, “Every time we identify a new part of how the malaria mosquito interacts with us, we’re one step closer to controlling it better.” Dr James Logan, who headed part of the research at the London School of Hygiene and Tropical Medicine was quoted as saying in the news.com.au online article.

So in summary, we need more people to people to start using Fasoap on their smelly feet …  while also spreading insect-killing fungi about. Interestingly while the fungal infection from the biopesticide can take up to two weeks to kill the host mosquito, during that time it significantly impairs the hosts ability to respond to host-related odour cues by flying up wind as well as a ‘suppression of olfactory receptor neurons tuned to 1-octen-3-ol, a mammalian odorant known to attract biting flies, including mosquitoes’[v]. It all comes back to the smell doesn’t it? And there was I believing the malaria mosquitoes were the kamikaze-esque villains but really they’re more akin to mindless zombies driven by their ‘noses’ ….. hmmm, now why didn’t I use that for a title?

So, malaria is and will continue to be fought on many fronts. While I have looked at some of the more scientific approaches, it is also clear from the extra reading I have done that an interdisciplinary approach is still required with collaboration with government and aid agencies. There is more to write in follow-up but I am now at the end of my word limit.

Take care,

the Domestic Scientist.


[i] <http://ec.europa.eu/environment/integration/research/newsalert/pdf/134na5.pdf> European Commission (2008) Encouraging innovation in biopesticide development.

[ii]community of researchers in more than 20 countries who are working together to understand how genome variation in human, Plasmodium and Anopheles populations affects the biology and epidemiology of malaria, and to use this knowledge to develop improved tools for controlling malaria’ http://www.malariagen.net/about

[iii] Smallegange R, van Gemert G-J, van de Vegte-Bolmer M, Gezan S, Takken W, Sauerwein RW & Logan, JG 2013,  ‘Malaria Infected Mosquitoes Express Enhanced Attraction to Human Odor’, PLoS ONE, vol.8, no.5.

[iv] ‘Stinky feet may lead to better malaria traps, help fight the mosquito-borne disease’ June 04, 2013.
Read more: http://www.news.com.au/technology/sci-tech/stinky-feet-may-lead-to-better-malaria-traps-help-fight-the-mosquito-borne-disease/story-fn5fsgyc-1226657371727#ixzz2Z1lnnpW5

[v] George J, Jenkins NE, Blanford S, Thomas MB, Baker TC, 2013, ‘Malaria Mosquitoes Attracted by Fatal Fungus’, PLoS ONE vol. 8, no.5, p.1.