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, especially the one about pay-walls.

Awesome picture from
Awesome picture from

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

Neat Science Thursday – Call for Papers

We interrupt our regularly schedule post for this important announcement. There are only 7 days left to answer the call for papers and save a scientist.

Don’t leave Andrew and Ben to fend for themselves amidst to all that water, sun, and sand.

The 2015 Pacific Symposium on Biocomputing will be held from Jan 4-8 on Kohala Coast in Hawaii! Andrew and Ben (together with collaborators Robert and Zhiyong at NCBI) are organizing the session on Crowdsourcing and Mining Crowd Data. For the session to be remotely decent, they need manuscript submissions. Submissions will be vigorously peer-reviewed and accepted papers will be published in an archival proceedings volume (fully indexed in PubMed), with a number of the papers selected for presentation during the conference. Please consider submitting your manuscripts describing biocomputing applications and methodological advances in crowdsourcing techniques or learning from crowd data. Andrew and Ben are going to PSB for the research, but will be forced to hit the beach if their session is cut short due to insufficient entries. Don’t expose them to be excessive radiant heat of the sun when they would rather bask in the cool, comforting glow of countless compelling powerpoint presentations.

Here are the details on how to help them:
Visit the PSB session call for papers page for useful details to determine if your manuscript is right for this session. Instructions on how to format and submit your manuscript are also included on that page.

Key Dates:

  • Manuscript submission: July 31, 2014
  • Notification to authors: September 9, 2014
  • Camera-ready papers due: October 1, 2014
  • Abstract deadline for posters: November 17, 2014
  • Conference: January 4 – 8, 2015

Session Organizers

  • Robert Leaman, National Center for Biotechnology Information (NCBI)
  • Benjamin Good, Scripps Research Institute
  • Andrew Su, Scripps Research Institute
  • Zhiyong Lu, National Center for Biotechnology Information (NCBI)

Neat Science Thursday – Love thy soil chemistry

So much of science is really about understanding and appreciating the beauty of nature, hence it seems strange to me how some people or companies (or both in the US since companies count as people now) paint the two as polar opposites. Though many of my previous posts have been a bit microbe-centric, I want to emphasize that the different scientific disciplines all relate to one another since science is about explaining nature, and nature does not fit into neat little compartments or categories.

Previously, I briefly covered the importance of microbes in nitrogen cycling for aquaponics systems, but a lot more than just nitrogen cycling is needed to keep plants healthy. Many plants also have a preferred soil pH, so it’s time to pay some respect to the study of chemistry!

If you’re an avid gardener, you probably already know that pH is a measure of acidity or alkalinity and that different plants grow better when rooted in soils of specific pH ranges. For example, blueberry bushes prefer slightly more acidic soils.

Many plants not only require a number of transition metal elements as nutrients (iron, copper, manganese to name a few), but also for these nutrients to be in a form that enables their uptake by the plant. For example, manganese is an important part of photosystem II in the photosynthetic reaction center, while copper is an important part of photosystem I. Love that plants take carbon dioxide and release oxygen? The manganese is important for that.

Simple photosynthesis overview
You probably already knew that Plants use water and carbon dioxide to produce energy and oxygen via photosynthesis
But did you know that manganese and copper play an important role in this process? This is one of several reasons Mn2+ is so important for plants

Plants are able take up manganese in its ionic form (Mn2+). In the soil, Mn2+ will often form salts with anions present in the soil, and many of these solid salts will be more soluble in acidic as opposed to alkaline conditions. This means that in acidic soil, the manganese may be more readily taken up by plants, which may help to explain why fruiting plants (in general) prefer a slightly acidic soil pH. Considering the amount of photosynthesis needed in order to synthesize all the sugars the sugars stored in the fruits. Copper and many other micronutrients are also more readily available in slightly acidic soils than they would be in alkaline soils.

And because chemistry is an awesome discipline that deserves a bit more love, here’s how to create your own pH indicator using red cabbage. It was one of the coolest experiments in the 7th grade science class, and may come in handy if you can’t afford a real pH testing kit for your aquarium.

Adapted from How to make Red Cabbage pH Indicator by Anne Marie Helmenstine, PhD.

Red cabbage contains a pigment molecule called flavin (an anthocyanin). This water-soluble pigment is also found in apple skin, plums, poppies, cornflowers, and grapes. Very acidic solutions will turn anthocyanin a red color. Neutral solutions result in a purplish color. Basic solutions appear in greenish-yellow. Therefore, it is possible to determine the pH of a solution based on the color it turns the anthocyanin pigments in red cabbage juice.

The color of the juice changes in response to changes in its hydrogen ion concentration. pH is the -log[H+]. Acids will donate hydrogen ions in an aqueous solution and have a low pH (pH 7).


  • red cabbage
  • blender or knife
  • boiling water
  • filter paper (coffee filters work well)
  • One large glass container


  1. Chop the cabbage into small pieces until you have about 2 cups of chopped cabbage. Place the cabbage in a large beaker or other glass container and add boiling water to cover the cabbage. Allow at least ten minutes for the color to leach out of the cabbage. (Alternatively, you can place about 2 cups of cabbage in a blender, cover it with boiling water, and blend it.)
  2. Filter out the plant material to obtain a red-purple-bluish colored liquid. This liquid is at about pH 7. (The exact color you get depends on the pH of the water.)
  3. You can make your own pH paper strips using red cabbage indicator. Take filter paper (or coffee filter) and soak it in a concentrated red cabbage juice solution. After a few hours, remove the paper and allow it to dry (hang it by a clothespin or string). Cut the filter into strips and use them to test the pH of various solutions.

Red Cabbage pH Indicator Color Chart
pH – Color
2 – Red
4 – Purple
6 – Violet
8 – Blue
10 – Blue-Green
12 – Greenish Yellow

That’s it! Go forth and appreciate the wonders of acid-base chemistry. Visit for more awesome chemistry that can be done at home.

Neat Science Thursday – Sleep is awesome!

Unlike many untested dietery supplements that are marketed for improving your skin, memory, immune response, etc; there is a free aid that has actually be studied in the context of human health: Sleep!

According to the CDC more than 1 in 4 Americans report not getting enough sleep, and 1 in 10 Americans have chronic insomnia.

For many people, sleep is a luxury they cannot afford; maybe it’s the new baby in the house, maybe it’s the long work hours forcing, maybe they are procrastinators exploring new avenues to practice their craft. Regardless of the cause, the consequences of sleep deficiency can be severe. Think of missing sleep as getting a paper cut–it’s not a big deal once in a while, but when it’s routine, you are opening up yourself for illness, irritation, and accidents.

Although sleep has already been known to play an important role in synaptic plasticity in the developing brains of kittens and in imprinting (memory) of birds the cellular mechanism by which sleep strengthens learning had yet to be elucidated. Then, in last month’s issue of Science researchers discovered that sleep was important for the retention of dendritic spines that formed under the context of learning a new motor skill (at least in mice, anyway). If you are cramming all night for that final exam….you’re doing it wrong! Study well, but get plenty of sleep if you hope to retain anything by test time. Given the importance of sleep on memory, is it any wonder why many FDA-approved anti-dementia drugs also affect the quality of sleep? In a recent article, researchers examined the potential role of sleep as a mediating factor affecting the observed association between post-traumatic stress disorder and hippocampal size differences.

Sleep deprivation has such a profound effect on the mind that researchers are considering its use as a model for psychosis!

In addition to memory, sleep plays an important role in immunity as well. In one small study (actually involving humans), sleep deprivation was associated with alterations in neutrophil populations–resulting in a low-grade pro-inflammatory state consisting of potentially immature neutrophils. This pro-inflammatory state that could exacerbate the symptoms of asthma and other hyper-allergic responses, but still fail to fight off infectious invaders due to the insufficient production of reactive oxygen species (ROS) by the immature neutrophils. Sleep deprivation has been associated with increased levels of cortisol (and other glucocorticoids), which can affect inflammation. Low levels of inflammation have been associated with depression, so it should be no surprise that sleep disturbances have been associated with mood disorders as well. Insufficient sleep has also been found to interact with the perception of stress and pain, which can affect the ability to sleep and result in the need to self-medicate using alcohol or other drugs.

Because of its effects on immunity, sleep may play an important role in regulating the gut microflora and affect gut and skin health. Sleep disturbances have been associated with inflammatory bowel disease and preliminary research on circadian rhythms in mice suggest that alterations in sleep patterns can affect the gut microflora. If sleep status can affect asthma, it is likely to have an effect on dermatitis and other hyper-allergic skin conditions. One review has even examined the potential relationship between sleep, inflammation, stress, and acne. Don’t want bags under those eyes? Don’t buy eye creams, get more sleep!

If you eat plenty of awesome veggies in order to feed your gut microbes, get plenty of sleep to keep that immune system working properly to maintain your microflora. If you have trouble sleeping, click here for some tips to help improve your sleep.