Journals #2: All Journals Big and Small. Why are there so many?

I’ve talked about what journals are like and how they got started, and now I’m going to talk about the sometimes overwhelming variety of journals available. In 2012 it was estimated that there are 28,000 journals devoted to publishing original research. Why are there so many?

As a profession, scientists have spent a lot of time and effort classifying things. This classification can help sometimes. If I want to know about today’s research in blood cells, I might read articles from The American Society for Hematology’s journal Blood. If I wanted to learn more about exoplanets I might read The American Astronomical Society’s journal The Astronomical Journal. These are examples of specialist journals edited and managed by societies dedicated to a narrow field. When I talked about peer review in the first post of this series I mentioned that when an editor receives a manuscript, that editor can reject it without any review. This can happen because the editor feels like the mission of the journal does not include publishing results in your field. The editor of Blood would likely reject a paper talking about a ninth planet for instance.

Other journals are incredibly broad publishing blood or planet research side by side. My impression is that these journals come in two flavors. One type (Like PLoS ONE) takes advantage of online publishing and includes whatever passes peer review while the other “prestigious” journals limits what they accept to find and publish what they consider the most amazing impactful research. This dichotomy lends itself to a sense that publishing in the later grants more prestige than publishing in the former. Publishing in Nature or Science (widely regarded as the most prestigious journals) is a goal of scientists in many fields and most of the time carries great weight when scientists apply for competitive jobs.

That is usually because these two journals have a high “impact factor” (number of times the articles in a journal are cited in future publications divided by the number of publications) has come up and been used to rank the value of publishing in any given journal. A ranking system isn’t necessarily bad, but the method used is pretty subjective. Because the “top tier” journals are rejecting papers to be more selective, “top tier” research is decided by editors who think the science is “high impact.” Of course, there is a difference between good science and bad science, but sometimes scientists forget to critically evaluate work in a top journal conflating prestige or impact with quality.

That said, there are journals that are better than others. Along with honest open access journals that publish anything that passes peer review, a class of journals sprang up that will publish anything that comes with the publishing fee. These journals are called predatory journals because they take the money of researchers responding to the pressures of publish or perish and put your data in a journal your peers or advancement committee won’t respects. Sometimes, researchers responding to the pressures of publish or perish will submit to these journals without knowing.  Sting operations lead by Science magazine and more recently by an independent journalist have shown an abundance of open access journals that will publish anything for money. Jeffrey Beall is a librarian at University of Denver who runs a blog with a long list of journals that he thinks are predatory. Critics of his methods point out his biases, but mostly see his criteria as a good starting point.

So if there are so many different kinds of journals and not all of them are reliable, how can we make sure we aren’t being lied to? To do that, we need to learn to critically evaluate each paper on its own merits. This may sound like a daunting task, but if you come back for my next article, I’ll give you tips and pointers to tackle the article behind the next big science breakthrough.

Bryan Visser
2013-12-04 14.06.58Bryan is a 2nd year graduate student studying DNA replication. He plans on making a career for science advocacy working at a museum or in Washington, DC. In his free time, Bryan enjoys board games and ballroom dancing.

Cool Stuff Last Week: miniature hearts, a new use for coal, and a possible new Alzheimer’s drug

Science is awesome, and it’s always changing. Here’s a recap of what happened last week.

  1.   “Micro-Heart Muscle” arrays may help us understand heart development and disease

Many scientists seeking to understand complex biological systems will use animals such as mice as a model. However, there are inherent problems with this approach. Mice, despite their evolutionary similarities to humans, are not, in fact, human, and many times we will work for years to cure mice of a disease only to find that the amazing new cure doesn’t work very well in humans.

Researchers in recent years have begun using tissue engineering to create new and better ways of modeling human systems. A research group from the University of California, San Francisco has created a new, miniaturized model of cardiomyocytes in hopes of being better able to model human conditions. The new Micro-Heart Muscle system is not the first three-dimensional heart stem cell model, but it is the first time someone has created a small scale, physiologically relevant cardiac model. These tiny hearts use only a small number of cells, meaning it is a cost-effective system, and they act like real hearts, organizing into complex fibers that beat and can respond to signals that a human heart would respond to. The group hopes these tiny hearts will be able to be used for studying development and testing drugs in the future.

  1.   The hot new electronics material? Coal.

Sometime during the Bronze Age, humans discovered coal, and we’ve been setting it on fire ever since. For thousands of years, and particularly since the Industrial Revolution, coal has been seen as a practical and readily available source of fuel. However, scientists at MIT are looking at coal in a new light – as an intricate material that could be used in sophisticated electronics.

In a paper published in NanoLetters, a team led by Jeffrey Grossman describes in details the chemical and electrical properties of thin film of coal. The most interesting result of their study was that, through simple processing techniques, the same coal films could be made more or less conductive. This makes coal a versatile material that could potentially be used for many applications. As proof of concept, the team used their coal-based films to create a simple heating device.  

  1.   A protein called IL-33 reverses Alzheimer’s symptoms in mice

A new injection that may help treat Alzheimer’s is about to enter clinical trials. The injection is a protein, known as IL-33, that is produced by many cell types, including neurons. A research group from the University of Glasgow found that an injection of IL-33 into mice with Alzheimer’s-like syndrome was enough to improve the memory and cognitive function after only a week.

The protein purportedly works by activating immune cells in the brain. These immune cells then target amyloid plaques, toxic lesions that build up in some people’s brains as they age and are believed to be a major cause of Alzheimer’s disease. No one yet know why amyloid plaques build up, but they are considered an important target for curing the often devastating condition.

Like I mentioned earlier, treatments found using mouse studies don’t always (or even usually) translate into effective human treatments. Regardless, the IL-33 injection is slated to begin the rigorous and lengthy clinical trial procedure to determine whether it might in fact prove useful to humans with Alzheimer’s. For now, we will consider this finding another piece in the puzzle of understanding a complex neurological disease and hope this treatment fares well in trials.

Jessica (Editor)
10891702_10152475816767115_155735200795992761_nJess is a fourth year biology PhD student who studies the liver and its regenerative capabilities. In her admittedly limited free time, she enjoys traveling, writing, and being outdoors.

Journal Series #1: What are Journals?

At Science ACEs, we believe in science for all, and while we enjoy sharing the latest in science news and figuring out how accurate our favorite tv shows are, we also take an interest in improving the conversation between scientists and non-scientists.  Scientific literature is highly technical and specialized and may feel out of reach to those unfamiliar with it, but  if you know how to find it, then with a little bit of work you can look at data and draw your own conclusions, freeing yourself from pundits and marketing ploys.

This will be the first part of a series of posts I’ll be making on how to approach and conquer scientific literature. I’ll start with what a journal is and how scientific studies go through peer review to enter journals. After that I’ll talk about the variety of journals out there, how to find them, what to look out for. I’ll finish up with the general structure of a journal article and tips for getting through jargon and interpreting results. For today though, we’ll go through a journal and point out some of its features and talk about peer review.

I have a physical copy of Science magazine in my hands. New issues come out about every week. As I flip through it, it seems like a normal magazine: Table of Contents, lots of advertisements, science news and opinion pieces. Eventually I reach the original research, presented in dense jargon and information-rich pictures. Science covers a broad range of topics, so I see work on cholesterol a few pages away from multiphoton entangled quantum states (whatever that means). Where did these types of magazines come from and how did they become this way?

The first scientific journal started unofficially in 1665 by the Royal Society as a way to keep records of their meetings. Philosophical Transactions of the Royal Society was a means for people who could not make it to London to still be a part of the scientific community and keep aware of advances. Journals gained in popularity as an alternative to frequent correspondence by mail. Another function of the academic journal was to set a record of who discovered something first. Scientific prestige is granted to the first person to discover a phenomenon, so an orderly method for determining precedence became necessary.

A formalized system of peer review was later added likely to protect journals from faulty sciences. Peer review means that if I want to publish a result, I must convince a few of the experts in my field that my science is sound and that my interpretation of results is proper. First, I submit my paper to the editor of a journal I want my work to be shown in. That editor looks at my paper and decides if it’s something the journal would be interested in publishing. If yes, the editor sends it off to reviewers who have a basic understanding of my field and would be likely to be able to critically evaluate my work. The reviewers are kept anonymous to me to prevent retribution for an unfavorable review. The editor gives me back the reviewer comments and I try to address them. Sometimes the reviewer asks for a section to be rewritten for clarity or sometimes they ask for additional experiments that they feel are necessary. If I can then satisfy the reviewers and the editor my paper is published and will appear in that journal. Hurray!

Scientists love to complain about peer review (especially reviewer 3), but without it the quality of publications would surely fall. Peer review is a means of keeping science honest. Pressure to publish is causing some researchers to submit papers to journals who do not use peer review and instead print anything as long as they receive their publishing fee. Next time, I talk more about these fake journals and how they are causing trouble for science and leading to confusion between scientists and nonscientists.

Bryan Visser
2013-12-04 14.06.58Bryan is a 2nd year graduate student studying DNA replication. He plans on making a career for science advocacy working at a museum or in Washington, DC. In his free time, Bryan enjoys board games and ballroom dancing.


Virtual Reality sounds cool, but how does it work?

Ever want video games to feel more realistic? Ever wish you could go to a work meeting but stay at home in your pajamas? Ever want to walk around another country from another century without plane tickets or time machines? Virtual Reality (VR) aims to bring consumers an immersive experience wherever they are. Just put on your headset and be whisked to another reality. VR is becoming more and more popular as a form of entertainment, but also is being used for training purposes for surgeons and fighter pilots. In order for VR to feel like another reality it needs to respond to your movement and allow you to interact with the virtual environment. So how do these headsets work to allow you to do those things?


Examples of VR headsets including HTC, Razer’s OSVR, and FOVE. Obtained from here

Most basically when I move my head, while wearing the headset, I expect what I see to change. If my virtual friend is behind me, I want to turn my real head around and see them. This requires head tracking from the headset. Headsets use two pieces of technology to accomplish this. Just as smartphones rotate screens and count steps, the headsets have gyroscopes and accelerometers that measure tilts and changes in the motion of your head. Since your phone already has these apps available for download, a cardboard housing can turn your smartphone into a basic VR headset. For greater head tracking, headsets like the Oculus Rift and PlayStation VR make use of a camera trained on LEDs to tell what direction you are looking in. Even more advanced is the development of eye-tracking. With this, you can keep your head still and only moving your eyes, change your field of vision. Eye tracking makes things you may take for granted like eye contact and blurring things you’re not focused on possible.

The ability to move through the environment is also essential for immersion. If, for instance, you want to peek your head around a corner without walking forward and turning, some mechanism needs to track your motion through space. Desktop solutions to this involve attaching extra positional sensors to the headset; but if you want to walk around in your virtual environment without using a video game controller you will require some serious hardware. VR treadmills want to strap you in and let you walk free. On the treadmill, sensors in the floor react to where you try to move but the treadmill belt keeps you from walking into any real-life walls.


A person experiencing VR. Obtained from here

In order to interact with objects in the virtual world users are given hand-held controllers that interpret motion and grips. Like other video games, these controllers give you buttons to allow your character to do all the things they need to for the game or simulation, but they also include magnetic fields to track motion and get precise spatial and orientation data on where the controller is positioned. This lets you (in real life) reach down and (in virtual reality) pick up objects. Any training simulation whether it’s surgery or juggling needs to give you this sort of feedback on your hand motions. The cherry on the immersion sundae is binaural audio. This technique records and plays sounds that let you hear sounds coming from above or below you and more impressively lets you hear things as if they are far away, not just quietly. So imagine a simulation of an Amazon jungle. You hear birds squawking above and look up to see them flash by. There are vines hanging down blocking your way but you can push them aside and keep on your trek.

When VR gets fully worked out, it won’t just be for games. As I mentioned before the ability to immerse doctors and soldiers in situations they want to be prepared for, while still having the ability to hit reset if something goes wrong, will save time,  money, and likely lives. Other applications of VR include tourism (travel anywhere instantly), immersion therapy (expose yourself to your fears in a controlled, safe environment), and education (what do things look like at atomic scales?). Some even propose virtual reality capable of fundamentally changing our economy to one where we never need to leave our homes. Whether that becomes a reality or not, virtual reality is being developed to produce as lifelike an experience as possible,which will constantly blur the line between what is digital and what is real.

Bryan Visser
2013-12-04 14.06.58Bryan is a 2nd year graduate student studying DNA replication. He plans on making a career for science advocacy working at a museum or in Washington, DC. In his free time, Bryan enjoys board games and ballroom dancing.


Cool Stuff Last Week: Brain Chips, Solar Panels, and Wobble.

Science is awesome, and it’s always changing. Here’s a recap of what happened last week.

  1. Brain chip restores arm and hand movements to paralyzed man

Most of us don’t think a whole lot about what exactly happens when we open a door or type an email. Our brain and spinal cord do the complicated work of translating intent into action. But for quadriplegic people like Ian Burkhart, neural signals can no longer traverse the spinal cord, so the limbs no longer respond to commands like “pick up that fork.”

This is why Ian and a team of researchers at Ohio State University spent over a year working out in excruciating detail exactly how the human brain coordinates muscle movement in the wrist and hand. A chip in Ian’s motor cortex picks up neural signals and relays the signal to a computer program – that’s the easy part. The hard part was training the program to translate those signals into reliable motions. The team spent 15 months working with Ian on just six distinct hand and wrist movements until the computer could interpret them accurately and consistently.

Once the computer decodes the signal from the chip in Ian’s brain, it passes the message on to an electronic sleeve on Ian’s arm. The 130 electrodes on the sleeve stimulate Ian’s muscles, allowing him to move his own arm at will. Ian can pour water from a glass, swipe a credit card – and even play Guitar Hero. This is the first time an intracortical device has been used to restore function, in real time, to a quadriplegic individual. Although more work is needed before the system could be used on a broader scale, it has exciting implications for the future of treatment for paraplegic individuals.

  1. Solar panels that run on rain

If there’s one glaring problem with solar panels, it’s that they require, well, sun. They’re not the most realistic energy source if you live in Seattle. But now, researchers in Qingdao, China have created a solar panel that generates energy rain or shine. This solar panel is coated in a very thin layer of graphene. When rain hits the graphene, it results in a dual layer which generates energy via an electron charge transfer. This technology may need a little work before it hits the market – the solar-to-electric conversion efficiency is only 6.5%  – but given a little development, these new solar panels may provide a clean energy solution for rainy climates.

  1. Wobble baby: climate change affects how the earth moves

According to a new study from NASA, the earth is experiencing a rapid change in the way it moves about its axis. The earth naturally “wobbles” a bit on its axis, drifting east and west a little as it spins. Since 2000, the Earth’s wobble suddenly shifted course and began heading east at a rapid rate. Last week, scientists from NASA’s Jet Propulsion Laboratory published a paper detailing how shifts in Earth’s water distribution affect this drift.

They identified a number of interesting findings to help explain the shift. Massive loss of ice sheets in Greenland push the spin axis east, while loss of ice from West Antarctica and gain of ice from East Antarctica contribute to the shift. Perhaps most importantly, loss of water from Eurasia due to long-term drought has had a major effect on Earth’s wobble. This harmless shift nonetheless highlights the major impact global warming is having on our world.

Jessica (Editor)
10891702_10152475816767115_155735200795992761_nJess is a fourth year biology PhD student who studies the liver and its regenerative capabilities. In her admittedly limited free time, she enjoys traveling, writing, and being outdoors.

Be Amazed

While in the park on Sunday, I noticed a child jump for joy as she threw a paper airplane into the air. I then remembered a profound bit of wisdom from a famous scientist. I’m not going to mention his name, but he was famous enough that my undergraduate Biology professors drove 3 cars of interested students 20 minutes to hear him speak at another college.

His talk was decent,  but the most memorable part for me was the Q and A following the talk. A portion of his talk was dedicated to the importance of conveying information about the environment to the general public. Naturally, someone in the audience asked a question about how we can get children excited about science in the age of computers, smartphones and entertainment at the fingertips.

His answer boiled down to “Let the kids explore!” He said when he was a kid he would go down to the pond and catch frogs in a bucket. He didn’t just walk on a nature hike with every tree and fern pre-labeled; he just wandered around in the woods. In short, he advocated we simply need to expose kids to nature and let them run wild. I think he would have approved of this video from Nature Explore.

Looking back in my life, I can relate. When I was young I spent a decent portion of my time exploring the woods behind my house, or catching fireflies at night. What’s more, I’ve heard similar things from scientists in other fields. I have heard a Nobel Prize winning chemist speak poetically about “playing” with chemicals as a child, by consulting a large book of chemistry and performing reactions that wouldn’t blow himself up.

So why do I bring this up now?

It’s ok to be amazed by science. For people working in laboratories, listening to discoveries on the news, or even hearing politicians argue about the state of science, science itself can seem very dry. It’s as if science is something to be afraid of or something that requires constant vigilance. But there is another aspect of science. For me, science is the art of understanding how the world works, but, like any art, it is ok to step back and breathe for a second. The biologist can admire the soft glow of the GFP or the dance of a folding protein, the chemist should listen to the symphony of the bubbling chemicals or the light show of a reaction, and the field researcher can stand in awe of nature for a moment even as he or she documents it.

For those of us who do science professionally, it’s important that we remember this not just for our own sanity (to remind us why we do science),  but also that this is what gets people started with science. Just as seeing a beautiful painting may inspire a child to paint, seeing a chemical reaction may inspire a child to try science on their own.

And kids can accomplish great things – they don’t have to wait until they’ve been through twenty years of school to come up with the next amazing idea. Recently Marvel Entertainment revealed the finalist of the Captain America Civil War Challenge, a contest for girls ages 15-18 to submit innovative ideas for STEM based projects. Just watching the video, I was amazed at the ideas these young women have developed. While they are high school age, you can bet that they had an existing passion for science that has developed over time, and didn’t just suddenly decide to participate in the contest on a whim.

So today, whether you are doing cutting edge research, simply making a piece of paper fly through the air, or even just watching the clouds in the sky, take a second to take a deep breath and for just a moment, let yourself be amazed.

The Motley Advocate (Editor)
Motley Advocate is a Christian, a biologist, a writer and an amateur at many other things. He doesn’t have a twitter but you can e-mail him at