Why do people Mark2Cure?

Why do people Mark2Cure? | The Su Lab.

Mark2Curators have been busy! Over the weekend, our volunteers brought the current beta experiment from about 28% completion to over 50% completion. We’ve gotten excellent feedback from you and are working to improve on the issues and suggestions you’ve sent us! Thank you and keep them coming!!!

We're at 56% complete as of this morning--double where we were last Friday Morning!
We’re at 56% complete as of this morning–double where we were last Friday Morning!

We now have over a hundred registered Mark2Curators who have shared compelling reasons as to why they Mark2Cure.

If we categorize the reasons, they look something like this:

Why do people Mark2Cure? If we categorized it, people Mark2Cure because...
Why do people Mark2Cure? If we categorized it, people Mark2Cure because…

We know all of our Mark2curators are altruistic, else they wouldn’t be contributing, but many have their reasons for doing so. For over half of our Mark2Curators, the primary motivation for contributing is to help others! How awesome is that? About half of our Mark2Curators were motivated by their interested in health and science. About 25% of our Mark2Curators were motivated by disease ties, with >70% of the disease ties being rare diseases. If you’re wondering why the sum of the percentages is over 100%, it’s because many reasons cannot neatly be contained by a single category.
If a picture is worth a thousand words? What's a picture formed from the words of our Mark2Curators worth?  ...priceless!
If a picture is worth a thousand words? What’s a picture formed from the words of our Mark2Curators worth? …priceless!

This post was originally written for Mark2Cure and can be viewed in its entirety here.

BioGPS news, an awesome recipe, and election reminder

A record 99,729 queries were made to BioGPS this past October–just 271 queries shy of 100K! Curious about BioGPS users are studying? So are we! If you’ve published and article using/citing BioGPS, share your finding with BioGPS and have your work highlighted in the BioGPS featured article series. For November, we have some interesting spotlights on BioGPS plugins scheduled as well as some interesting research coming from BioGPS users. Look forward to it!

Also, if you like gardening like I do, but don’t always know what to do with the food you’ve grown here’s a recipe for using up all that zucchini from Jenerallyfit.com a side project nutrition/fitness site by a scientist who has done some brilliant work in viral pathogenesis.

    Zucchini Marinara

      2 Zucchini
      3 Servings of your favorite marinara sauce (we used Rao’s)
      4 Italian chicken sausages

    Cut zucchini using spiral vegetable cutter and heat until tender. Heat sliced chicken sausage (or topping of choice) and marinara sauce in a separate pan. Mix together and that is it!

    Makes 2 servings at approximately 370 calories per serving.

Visit her site at Jenerallyfit.com to see some awesome pix of this easy and nutritious meal.

Finally…if you are in the US, don’t forget to vote. You forfeit your right to complain about US politics if you don’t vote.

Chocolate chia seed pudding

What do PhD’s do in their spare time? In Jenna’s case, it’s helping other people get healthy and fit. She just started her own site at: http://jenerallyfit.com/index.html and has posted some fabulous recipes.

This looks ridiculously tasty: Chocolate Chia Seed pudding

This pudding is rich and creamy and only takes a few minutes of prep time. Chia seeds (yes, like from the Chia Pet!) can absorb up to 12 times their own weight in water, which helps keep you hydrated and feeling fuller longer. They’re also a great source of protein, fiber and Omega-3 fatty acids. Here is the recipe:

  • 2 oz Chia seeds
  • 8 oz almond milk
  • 2 tbsp cocoa powder
  • Stevia to taste

Mix together ingredients and let sit in the fridge for at least 15 minutes to overnight. The longer it sits the thicker it will get. Makes 2 servings at around 180 calories per serving. You can definitely mix it up by using your favorite milk (coconut, skim) and/or sweetener (honey, agave). If you’re not in the mood for chocolate you can add almond or vanilla extract with cinnamon and raisins instead of cocoa power for an easy rice pudding. Top with your favorite fruit and enjoy for a healthy breakfast or dessert.

Chocolate Chia Seed pudding courtesy of JenerallyFit

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 – 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
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 – 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