Neat Science Thursday – Perpetuating Pseudoscience

The myths touched on in a previous Thursday post are extremely persistent, but aren’t usually very harmful. In contrast, the pseudoscience perpetuated by many supplement peddlers, like Dr. Oz, can have serious adverse effects. Hence it was no surprise that many in the scientific community applauded the congressional grilling of Dr. Oz, and John Oliver’s informative yet bleakly entertaining follow up.

While John Oliver did an excellent job highlighting the issue, no one actually believed that something would be done about the use of pseudoscience in selling dubious dietary supplements.

Proving everyone right, Business Insider just published an article on a new trendy supplement–Activated Charcoal:
With the change of the seasons (in this case, summer to fall), it always seems like people feel the need to detox their bodies.

A lot of the recent detox buzz is around activated charcoal. Charcoal, however, isn’t really new – it’s been around since long before the 19th century, when both the ancient Egyptians and Greeks used it as a multi-purpose poison and disease antidote.

Today, it’s most commonly used in emergency settings to treat accidental poisonings or drug overdoses. Well, that’s until someone decided it would make a great supplement for a detox program, anyway.

Seriously? Activated Charcoal as a dietary supplement? Disturbing. And just when you though the pseudoscience nonsense can’t get any worse, it turns out that Consumer Reports has may be pandering to Dr. Oz too, adding to existing concerns about Consumer Reports steady slide into promoting pseudoscience.

The Genetic Literacy project received a memo regarding Dr. Oz’s visit to Consumer Reports from a former senior editor who parted ways with CR after getting “fed up with the woo”. ‘Woo’ refers to pseudoscience, magical thinking, or quackery.

Neat Science Thursday – Scientific communication is hard

For my dissertation research, I studied the mechanisms of viral persistence in the central nervous system using an in vitro model consisting of picornavirus infections of differentiated and undifferentiated murine neural progenitor and stem cells.

To some of my non-science friends and family, that explanation sounds something like, “I studied blah blah blah, miscellaneous pretentious scientific jargon, blah blah.”

Of course, they would still have no idea what I studied, and any further attempts to explain would be met with that kind, patient look that people give you when they’re bored but are too polite to walk away.

So I would tell non-science people that I studied “how a virus hides in the brain for a long time, and the consequences of having a virus hiding in the brain using mouse stem cells”.

This explanation will elicit much more interest, but can sometimes get distorted when described second-hand to others since it’s not as accurate. Also, there may be some fellow scientists who will think you lack professionalism, or don’t know what you’re talking about if you use this sort of description.

If you think about it, there is so much jargon specific to each field of study, it’s actually pretty impressive how well scientists have been able share information across disciplines. Of course, there is always room for improvement in that arena, especially since researchers primarily disseminate their findings via scholarly articles, keying them for easy search amongst fellow researchers in their discipline. The differences in jargon sets contributes to the difficulty in finding research articles outside your field of research which contain research findings that could have important impacts in your own work. It’s also why there has been a lot of interest in annotating research literature and making it more searchable (Go! Go! Mark2Cure) as well as creating an open database where information contained in research literature can be formally structured around a set of shared ontologies (Go! Go! Wikidata.

It’s also great that these findings are becoming more available as funding agencies help to drive open access policies enabling the public to finally access the research paid by tax/donation dollars. But open access does not mean accessible if we consider the sheer volume of jargon that must be learned in order to read and understand scholarly articles. How can we expect tax payers to support research if they are locked out on so many levels? Now before you argue that ‘people need to take personal responsibility for their own education’ or ‘the articles aren’t really hard to read if you actually put in the effort,’ ask yourself this, ‘Am I dismissive of people science communicators that communicate science via non-traditional channels (ie- non-academic journals)?’ If your answer is ‘yes’, you waive all rights to complain about the scarcity of research funding.

If your answer is ‘no’, consider contributing your expertise to a truly accessible knowledge-base/medium like Wikipedia. Efforts are already under way to make information on every human gene of interest publicly available on Wikipedia (the Gene Wiki initiative), and greater participation is needed from scientific community.

For those of you, researchers or not, who ARE able to communicate science with such elegance, enthusiasm, poignancy, and precision–especially those of you on non-traditional channels like Science 2.0, twitter, etc.–thank you for using your talents to engage the public so they can see how their money is being spent. You are awesome! The rest of us will just have to keep trying.

Neat Science Thursday – Too Much Information

Personalized medicine has been a goal for a growing number of biomedical researchers over the last twenty years. Considering the fact that biomedical research literature on personalized medicine has grown from 5-10 articles/year in the 1980’s to over 2500 articles per year since 2013, incredible progress has been made towards this extremely challenging goal. For personalized medicine to happen, at least two elements are necessary: 1. A means of acquiring personalized data is needed, and 2. A means of integrating, analyzing, and applying that data. The explosive improvements in the amount, quality, efficiency, and cost-effectiveness of obtaining personalized data , creates a huge challenge in the integrating, analysis, and application of that exponentially growing body of data available. Thus, the challenge of personalized medicine primarily lies in the integration and analysis of ‘Big Data.’ Yes, there is always room for improvement in data acquisition, but all the growing data is problematic if it cannot be effectively utilized. Researchers from all over the world have been working on analysis tools in order to better extract useful information from the growing available sets of omics data, and [Warning: shameless plug alert] The Su lab’s Omics Pipe is one attempt to automate the best practice multi-omics data analysis pipelines. [End shameless plug]

Barbour Analytics published a fascinating post on the N-of-1 problem in Big Genomics. It is a great read for anyone interested in personalized medicine, rare diseases, big data, and bioinformatics. Here is a teaser to encourage you to take a look at the original post:

How do we assess the impact of a single novel mutation, or a set of novel mutations, unique to an individual? This is the N of 1 problem in Big Genomics. Statistics, and statistical genetics rely on summary, on binning the patterns of populations of individuals into categories of adequate size that we can compare groups using standard metrics like mean, median, mode, standard error, and in more elaborate frameworks use more sophisticated metrics like moments, edges, vectors and ridges.

The N of 1 problem in Big Genomics will require modeling approaches, to construct models of the genome, and make projections on the likely function of single de novo mutations, and suites of these private mutations. Robust modeling efforts in this area will be a major challenge in the era of genomic medicine, and personalized medicine. At present we are effectively constrained to study mutations that have recurred throughout evolution. As our population grows, as the number of persons under care, and participating in genomic medicine increases, we will need to address the private mutation issue head on.

We can look to cancer genomics for some guidance. Cancers are a genomic disease, with both inherited and de novo elements, and direct sequencing of genomes often reveal unique mutations that lead to unique cancer profiles. This field has the advantage of seeing a clear disease manifestation in the form of tumor growth, often restricted to a tissue or cell type. This helps make more direct inferences about the likely function of the novel mutation.

That said, we face the inherent limitation that a mutation may be unique, or at least rare, and for this reason it is difficult to use traditional statistical approaches, approaches that rely on summary, on the behavior of groups of instances. While the genotype information may be limited to one person in these instances, we can assist ourselves in this effort by capturing more information about clinical and biological phenotype. Detailed phenotypic characterizations of a tumor or affected tissue – extending to the transcriptome, kinome, metabolome, cytokine profiles, cell morphology and indeed clinical status itself, can help us perform a sort of reverse interpolation to infer the function of the single N of 1 de novo mutation. While the mutation may be unique or rare, the disease manifestation itself may be common, or at least share key features with other maladies.

Now go read the original post here: ‘Private Mutations’: The N of 1 in Big Genomics — Barbour Analytics.

Neat Science Thursday – Science communication matters

Tweets about science flooded twitter feeds again yesterday when Science released its list of the top 50 scientists on twitter and their corresponding K-index. If you haven’t heard of the K-index, you’re probably not on very high on it. The top 50 list received an enormous (and rather negative) response in the twittersphere. Why? Aside from obvious flaws of only relying on twitter followers and neglecting to include a lot of great female scientists, the top 50 list revived the reviled K-index!

Scientists that use twitter already took the k-index out of its self-imposed isolation, slapped it with a failing grade as a joke, highlighted its egregious mistakes, directed it to use real data before injecting it with a lethal dose of reality and leaving it to die. Many scientists that use twitter lambasted the K-index because they knew how useful it could be especially for sourcing articles (#icanhazpdf anyone) that are NOT open access and for outreach.

Contrary to popular belief, many scientists spend a lot of energy and effort in outreach because they understand and acknowledge the importance of scientific communication. Don’t think science communication is important? Consider how it affects the parent’s decision on whether or not to vaccinate a child. Science communication isn’t exactly easy either.

Don’t do enough of it (it being sci-comm, of course), and someone else will step in with grossly misleading headlines on how your research shows that aspirin cures cancer. Do too much of it, and fellow scientists will disrespect you and remind you that your place is back at the bench (K-index anyone). Do it poorly and you will have the same results as not doing enough, or you will be ignored to the point that when someone confirms your findings it will look completely like a huge discovery rather than an incremental one.

Those in science that are able to communicate science with elegance, enthusiasm, poignancy, and precision are praiseworthy. Hats off to those of you who do it so well–that means you, GeneoTW writers, Science 2.0 and other science bloggers. You are all awesome! For the rest of us, we’ll just have to keep trying.

Now go back to tweeting great science, people.

Neat Science Thursday – Growing Science with Games

Gamification has become increasingly useful in getting people involved in science. Everyone can now contribute to science or learn more about science by playing fun and interesting games. Fortunately, you do not have to search very hard in order to find these awesome citizen science games because Chandra Clarke has already compiled them into an extensive list on her site. Here is just a small sample of the games that are available:

Astro Drone – Created by the European Space Agency, fly your Parrot AR drone in virtual space and compare yourself with real-life astronauts. Data from your successful flights will be used to train robots on how to navigate their environment. Website: http://www.astrodrone.org/.

Apetopia – Run over a landscape and then choose the door with the colour that best matches the sky at that moment. Collect coins and avoid obstacles too. The game helps determine perceived color differences; player choices are used to model better color metrics. Website: http://colors.htw-berlin.de.

Beat the Bots – Are you smarter than a spambot? VouchSafe has built an anti-spam program that uses the way humans think to try to outsmart spammers. Draw a line with your mouse to join an object to its best match, or circle the object that doesn’t belong. Yeah, okay, this isn’t really citizen science, but defeating spam is definitely for the greater good, don’t you think? Facebook: https://apps.facebook.com/beatthebots/

Cell Slider – Join the effort to defeat cancer by reviewing images to spot cancer cells. http://www.cellslider.net/

Collabio – Participate in social psychology research. Collabio is a Facebook application that wants you to guess tags that other friends have used to describe an individual. Points are awarded according to the number of other friends who have agreed with each tag. Facebook: http://apps.facebook.com/collabio/

Cropland Capture – Want to help improve the world’s food security? Help to improve basic information about where cropland is located on the Earth’s surface. Website: http://www.geo-wiki.org/games/croplandcapture/

Dizeez – Help researchers link various genes to diseases. The game is very simple: You are shown one gene name, and five diseases. Pick the disease that is linked to the gene to get points, and get as many points as you can in one minute. Website: http://sulab.scripps.edu/dizeez/

There are loads and loads more games so check out her Ultimate list of Citizen Science Games

More citizen science games can also be found on the Games for Change website which seeks to use gamification to catalyze social impact. Look under the STEM category, though science-related games can also be found under the other categories like ‘Environment.’ Many of these games are more on the science educational side rather than citizen science, but citizen science games like Foldit are sprinkled around the site.

If you prefer RPGs, try “Citizen Science” or “Oncology” on <a href="http://www.brainpop.com/"the BrainPop site.

Finally,

Neat Science Thursday – citizen science is a solution

In case you missed it, Caren Cooper et al. just published a fascinating research article on PLOS One (it’s open access, so check it out!) detailing her investigations on the contributions of citizen scientists in ornithological (bird) research. In this article the researchers aimed to “evaluate the use and confidence of citizen science in advancing understanding in an important area of ecology and global change research” by attempting to:

1. Quantify the scientific contribution of citizen science to research on birds and climate change
2. Assess whether professionals held volunteer-based research in equal regard to research by professionals
3. Evaluate the extent to which citizen science was readily visible or noted in the focal studies

 
In other words, the authors were attempting to see how important citizen science was to a particular area of research, and whether or not the contributions of citizen scientists were sufficiently acknowledged in publications. What they found was that data from citizen scientists were useful (and even critical in some projects) for this area of research. Unfortunately, the lack of consistent terminology acknowledging these contributions may have undermined the perceived impact of citizen scientists in this area of research. They went further to suggest that other research areas such as invasive species research may also benefit greatly from the “invisible prevalence” of citizen scientists.

Talk about timely! MJ Epps et al. just published a research article on the cryptic invasion of Asian camel crickets in North American houses. Fortunately, the researchers were upfront about their use of citizen scientists as they, “launched a continental-scale citizen science campaign to better understand the relative distributions and frequency of native and nonnative camel crickets in human homes across North America.” Oh, and you can read intriguing their open access article here: Too big to be noticed: cryptic invasion of Asian camel crickets in North American houses.

The problem of finding citizen science papers in this research area described by Caren Cooper et al. is by no means unique to citizen science and ecological research. All research areas suffer from insufficiently annotated publications making finding the right articles a growing challenge. While one solution may be to encourage researchers that utilize citizen scientists to use the term “citizen science” in their research publications, this will not solve the annotation issues that thrive in the existing and growing body of research literature.

Given how citizen scientists have solved protein structures, mapped neurons in the brain, and analyzed astronomical images on an unprecedented scale, perhaps the solution to the annotation issue in research literature lies in citizen science as well.

Neat Science Thursday – Open Access is Awesome

Twitter is a great resource for scientific inspiration, because the awesome scientists that regularly tweet share a lot of interesting articles, blog posts, and great content. One particular humorous piece was the link to the overly honest science methods pictures over at distractify.com, especially the one about pay-walls.

Awesome picture from http://news.distractify.com/geek/science/scientists-get-honest-about-their-methods

As hilarious as the image is, it draws attention to several important issues in research. First, is the excessive attention paid to indices such as Impact Factor, or citation-based indices. How often are highly cited articles cited without being read simply because they’re locked behind pay-walls? Why should the merits of a researcher judged primarily on their publications in highly cited, pay-walled journals? Let’s not even touch on how tweeting may impact the perceived respectability of a scientist by his or her peers.

If getting people to read the research article is of genuine interest, then open-access takes the cake. Citations may serve as a proxy for the number of people who read an article and found it valuable, if they actually had access to read the article. Otherwise, it’s just another number.

The Research Information Network (RIN) conducted an analysis of the articles published in Nature Communications and found that OA articles are cited more than subscription articles and attracted three times as many views as those only available to subscribers. More about this study here, see the report here or the full data set here because it’s open access, SO YOU CAN!

Of course, these issues may not be as important as getting and keeping a job. Unless academic institutions consider other metrics in their hiring practices, less established researchers may face considerable pressures against publishing in OA journals.

As one keen PhD candidate put it,

“Scientists applying for funding and positions are judged not only according to the quality of their work, but also where it is published. Having a single paper published in any of these high-profile journals can have a transformative effect on a career. If publication requires flashy work in fashionable fields then, so the argument goes, this offers the most reliable path to funding and permanent positions.”

View his insightful post about early career researchers.

And more recently, Erin McKiernan, an early career researcher, posted a compelling call for researchers to stand up for and publish in OA journals.

At any stage of your career, you have the right to stand up for what you believe in. If you believe in openness, stand up for it. Access to information is a human right, but it is often treated as a privilege. This has to change. And it will take all of us to make it happen.

See the rest of her post here

If these were not reasons enough, then consider the public good. How can grant-funded researchers expect the public to fund science (ie- grants), and not be able to see the results of their investments? One woman went to extreme lengths in order to gain access to research articles about the her children’s genetic disease.

“We spent hours copying articles from bound journals. But fees gate the research libraries of private medical schools. These fees became too costly for us to manage, and we needed to gain access to the material without paying for entry into the library each time. We learned that by volunteering at a hospital associated with a research library, we could enter the library for free. After several months of this, policies changed and we resorted to masking our outdated volunteer badge and following a legitimate student (who would distract the guard) into the library.”

Read Sherry Terry’s article here.

Or the story about the woman who deciphered her own genetic mutation. Who started by searching for biomedical papers on her disease, and then having to “scratched around in Google until she found uploaded PDFs of the articles she wanted.”

Convinced? Check out the list of journals to avoid like the plague.

And if you’re really dedicated, and work on a gene, join the Su lab’s efforts in expanding the publicly available knowledge base on human genes: Gene Wiki.

Neat Science Thursday – Crowdsourcing blues

As evident by a few of the previous posts on crowdsourcing science, wikipedia, and the GENE/Gene Wiki partnership, I think crowdsourcing science and citizen scientists are awesome! The speed with which a lot of interested non-scientists can sift through data is simply astounding!

In spite of all the positive features of crowdsourcing science and information (like wikipedia), there are also some interesting drawbacks. For example, wiki entries have been vandalized as part of a joke/challenge started by a comedian in order to make a joke/commentary on the wisdom of crowds, and more recently, users from government-related ip addresses have been systematically editing pages to reflect a particular political agenda. This kind of vandalism has prompted the banning of government ip addresses in the past.

But issues with crowdsourcing are not limited to just information platforms like wikipedia. Crowdsourcing competitions in order to foster participation and innovation have also been hijacked as covered in a recent (and very interesting) post on Science2.0.

According to the original post found at The Conversation about a new study:
“The research, published today in the Journal of the Royal Society Interface, found the openness of crowdsourced competitions, particularly those with a “winner takes all” prize, made them vulnerable to attack.

The researchers used game theory to analyse the trade-off between the potential for increased productivity from crowdsourcing a project, and the possibility of it being set back by malicious behaviour. They cited the DARPA Network Challenge as an example of a hijacked crowdsourcing competition, in which the organisers were left to sort through many fake submissions, including fabricated pictures of people impersonating DARPA officials….continue to the original post

Or visit the actual study publication (and hope your institution has access to it) if you want to read the original study.

Neat Science Thursday – More on yogurt

As discussed in Tuesday’s post about stipend-ready meals, yogurt can be a delicious, nutritious, and very cheap meal component. Although making yogurt is fun and easy, the science behind yogurt production is far from finished, and scientists are still uncovering interesting clues about optimizing the growth and fermentation of the microbes responsible in yogurt production. Although S. thermophilus has been found to provide formate and carbon dioxide to L. bulgaricus, which in turn provides peptides and amino acids to S. thermophilus, there are still many aspects of the symbiotic relationship that have yet to be understood. For example, Sasaki et al., previously found that yogurt fermentation by S. thermophilus and L. bulgaricus was less efficient at higher concentrations of dissolved oxygen in the milk (yet another reason to boil the milk when making yogurt, since heat reduces dissolved oxygen). Following up on this finding, Sasaki et al. investigated the how the presence of S. thermophilus might contribute to yogurt fermentation in terms of reducing the concentration of dissolved oxygen. In particular, Sasaki et al. found that the NADH oxidase of S. thermophilus was primarily responsible for the reduction of dissolved oxygen in the milk, promoting yogurt fermentation and the production of acids. You can read more about their interesting work, here since it’s an open access piece.

Although their research took an interesting detour, Sasaki et al. (like many scientists) was initially looking to optimize the taste and texture of yogurt. A recently published open access paper by Wu al. examined the ability of S. thermophilus to produce exopolysaccharides which could affect the perceived texture (and creaminess) of the yogurt as well as the bacteria’s able to survive and serve as a probiotic. To study exopolysaccharide production by S. thermophilus, Wu et al sequenced the entire genome of a strain of S. thermophilus: ST 1275. Once they determined the gene cluster essential for EPS production, they compared this gene cluster from ST 1275 to that of five other strains of S. thermophilus. Additionally, Wu et al. found important proteases and membrane transporters important for enabling S. thermophilus to thrive in milk (which has an abundance of proteins, but considerably less sugars.) Interestingly enough, Wu et al. also found stress response genes which are potentially responsible for the bacteria’s ability to thrive at very warm temperatures (remember, ~40C for making yogurt), and to survive under more acidic and cold temperatures (hence the bacteria’s ‘live and active’ status in refrigerated yogurt.) Thankfully, Wu et al.’s fascinating findings can be found on PubMed Central (PMC) where anyone can access it.

For more intriguing recent research on yogurt bacteria check out Ferdoisi et al.’s evaluation of probiotic survivability in yogurt exposed to cold chain interruptions, which reveals how temperature/storage conditions affect the ability of the yogurt bacteria to survive before you consume it. Again, these excellent researchers have made their findings available at PubMed Central

Bottom line. When nature gives us things we don’t understand like milk spoilage/fermentation, we can use science to understand, improve, and direct the process so we can better appreciate the wonders of nature.

Neat Science Thursday – Persistent Science Myths

In spite of existing research, there are some seemingly scientific myths that just can’t seem to be dispelled. Here are a few myths and some excellent posts discussing their merit and why they may persist.

Why Using 100% Of Your Brain Would Make You 0% Smarter.
If you’ve ever been on the freeway and saw the guy next to you holding his coffee with one hand, texting with the other, and steering with his kneecap while doing 80, you might find it quite plausible that humans only use 10% of their brain. This is actually a scientific urban legend, though, and quite far from the truth. The man you see is engaging many parts of his brain – the driving uses the cerebellum, the texting uses his frontal lobe, reading his texts uses his visual cortex. He finally heard you honking after his kneecap steered into your lane. That’s the temporal lobe. Although this man may not be using his brain very well, he is still using it. The myth that we only use 10% of the brain is roughly 100 years old, and is somewhat ingrained in our culture. functional MRI however shows that even with simple tasks….read more of Ariana Anderson’s excellent post on Science 2.0

“Waterlogged”–and the myth of 8 glasses of water/day
Water, water everywhere. Should doctors be telling people to drink more water as a public health issue? Hydration for Health, an initiative to promote drinking more water, held its annual scientific meeting in Evian, France, last week. The initiative has shown its fervour for water with recent adverts in the medical press, including the BMJ. The website states that its mission is “to establish healthy hydration as an integral part of public health nutritional guidelines and routine patient counselling so people can make informed choices.” It believes that “Healthcare professionals should be encouraged to talk with patients about the calorific content of SSBs [sugar sweetened beverages] when discussing lifestyle modification to manage overweight and/or obesity . . . Consumption of water in preference to other beverages should be highlighted as a simple step towards healthier hydration.” And healthier hydration is? “recommending 1.5 to 2 litres of water daily is the simplest and healthiest hydration advice you can give.” Hydration for Health has a vested interest: it is sponsored and was created by French food giant Danone. This company produces Volvic, Evian, and Badoit bottled waters. The initiative’s website is bold…read more from Margaret McCartney’s post on the BMJ’s website