Journal Club: What is a Stem Cell?

This is a new writing exercise in which I'll post about an article that was discussed in my lab's journal club. Recently, we read a new paper by some preeminent figures in the stem cell field.

The paper, No Identical ‘‘Mesenchymal Stem Cells’’ at Different Times and Sites: Human Committed Progenitors of Distinct Origin and Differentiation Potential Are Incorporated as Adventitial Cells in Microvessels, was published in June 2016, in the journal Stem Cell Reports. The full text of this open access paper is available here.

A new paper by Benedetto Sacchetti, part of recently deceased Paulo Bianco's research group, seeks to clarify some much needed points in the world of mesenchymal stem cells or MSCs, and their lack of universally accepted definitions. In fact, the authors also argue against using the term “MSC,” as it is misleading. They claim that stem cells should be named by their tissue of origin instead, because as shown, these cells retain characteristics of where they were isolated from, despite sharing some similarities.

An increasing number of stem cell clinics are popping up, claiming everything from anti-aging benefits to curing diseases. These clinics are pulling *something* out of people, calling this random slurry "stem cells," and injecting it back into clients. This is a false and dangerous practice. While stem cells have great therapeutic potential, there is still much work to be done in basic research before these claims can be verified or even tested. This issue is further complicated by some people in the stem cell field that claim “MSCs” can cure everything from stroke to osteoarthritis. While some of the research is promising, there is no clear definition of an “MSC," let alone well documented therapies.

In Sacchetti's paper, they clearly show that stem cells from different tissues have different abilities to differentiate, and are not ubiquitous, despite having some similar characteristics. The authors look at cells from four different tissues: bone marrow, muscle, the outer surface of bone, and umbilical cord blood. 

Currently, stem cells are isolated for research using proteins that sit on the surface of the cell. This paper shows that despite having similar surface markers, cells from different tissues have clearly distinct gene expression patterns, shown with two different clustering techniques. Each of the four types of stem cell retain a gene expression pattern that is directly related to their respective tissue of origin. 

Next, this paper explores the differentiation ability of stem cells from different origins. Only the cells from bone marrow or periosteum (also a bone-related tissue), were able to form new bone, complete with bone marrow inside. Cells from muscle did not make bone, and cells from cord blood weren't able to form complete bone marrow. The ability of a cell to make new bone, including bone marrow is a defining marker of a skeletal stem cell. 

Following this, they looked at the ability of these four types of stem cells to differentiate into muscle. As before, only the cells that were isolated from muscle retained the ability to differentiate into muscle, while the other three were not. This was also shown by looking at the ability of these cells to regenerate muscle after an injury, and again only the muscle derived cells were able to make new muscle. 

The overarching point of this paper is that cells from different tissues shouldn’t be uniformly referred to as “MSCs”, when they clearly show differences. Instead, they should be referred to by their tissue of origin. While there are some similarities, the inherent ability of each cell type to differentiate is different. 

Keep moving

Some people, (I have a specific former intern in mind) are scared to move forward. They don't know what to do. They may be working on an undergraduate degree and not getting the grades they want, because they know their studying technique isn't very good. Or maybe stuck in a job they don't like because they don't know what they want to do with their life.

I ask them for ideas, brainstorms. What do you want your life to look like? What classes do you do really well in? Why are those different? What things could happen today to make it a wonderful day?

They can often answer these questions, but don't know the next step. They're scared of doing something wrong, or worse, trying and then failing.

Seeing this multiple times and listening to people further along in their career than I have lead to the same conclusion.

Success is not the opposite of failure, it's the step after it.

Too many people I know are scared of failure. I want to say to them, "Failing is okay!" Failure happens. You can survive failure. It's lack of motion, lack of action that will kill you. It doesn't matter if the action you choose doesn't work the way you want it to. Once you start moving forward, you can more easily evaluate your position, and make changes to it. It's getting that first step that's the hard part.

I told my intern that was struggling with his grades, that it doesn't really matter what study habits he tries to change. The point is to change something, and see if it works. It may not. It probably won't. But he will  have tried something, he can check it off the list if it doesn't work and then try something else. He will eventually find a study method that works really well for him, and more importantly, learn which ones are a waste of his time.

A mentor said something that really stuck me: "It's like riding a bike, you need forward momentum before you can change direction." So get moving, fall a few times, fail a few times, and keep going.

2015 in Review & Looking Forward

At the end of 2014 I wrote a post about my goals for 2015, and revisited them  halfway through the year. Which did I accomplish and which will I carry to 2016?

Professional:

• Publish in a policy journal again - Sure didn't, although I did publish a first author research paper, and started writing a second one. I have some ideas for a policy paper, but need to make it a priority if I want it to actually happen. Research papers are a much higher priority, so this is a maybe for 2016.
• Plan & execute DC networking trip - I did a lot of networking this year, and met some really awesome people. My long term career goals have changed, so this is now off the list.
• Identify & explore specific science policy careers - I'm leaning more towards staying in academia and research labs, where I can still read, write, and think about policy issues. I still plan on exploring career options as the opportunities arise.
• Find session/panel to moderate at future conference - I found the professional society I want to be most involved in (American Society for Bone and Mineral Research), and am exploring how to do so in 2016.
• Finish strategic outreach plan for CCH - Done! Interesting side project, glad it's over.
• Co-moderate PhD Career Conference 2015 - Done! This was fun, stressful, and a great learning opportunity. I got to interact with all of the fantastic alumni we brought in. Now I have to decide if I want to help coordinate it again in 2017.
• New goal: Mentoring - We have new people starting in the lab this year. Rotation students, undergrads, and likely a new technician at some point. I enjoy mentoring and helping new people, and would like to continue to develop this skill. 
• New goal: Say no - I did a lot this year in terms of running student groups, moderating workshops, and volunteering. Most of it was fun, and I learned something from all of it. However, it was a lot to take on and I feel like my attention was never fully on any one thing. This year, I'm going to try the Derek Sivers approach of Hell Yeah or No. Unless it's something I'm super excited about, I'm going to pass. (Caveat: Considering my general enthusiasm for most things in life, this may not free up as much time as I hope...)

School:

• Submit F31 grant - Done! Submitted in December, which is a later deadline than originally intended, but it was a better grant this way. Now that I've struggled through this process once, I want to do it again. I'm hoping to be more involved in my PI's next few submissions, in addition to finding more grant writing opportunities for myself.
• Pass qualifying exam - DONE! The lead up was without a doubt the most chronic stress I've ever experienced. The exam itself was fun, in a weird way. I may write a more extensive post about this in the future.  
• Attend 2 conferences - Done! I actually went to three conferences in 2015, winning one poster award and two travel grants. I've been to enough conferences at this point that I'm going to be a little pickier about which I attend in the future. ASBMR is a definite, and I'd like to attend a Gordon Conference at some point as well.
• First author scientific paper - Done! Submitted, accepted, and already writing the next one.
• Read at least 1 paper per week - Not quite. I've been scanning more abstracts, but need to focus on more indepth reading. One of my goals for 2016 is to start blogging about our biweekly journal club. One comment from my qualifying exam is that I need to be more familiar with the literature. 
• New goal: Push my own research forward. My most recent papers were from finishing projects that had started in the lab before I joined. Now that I'm generating a decent amount of my own data, I need a broad outline of what needs to be done before this can be written up.

There are also a number of personal and fitness goals for 2016, but those are currently in flux, and don't seem as interesting to blog about. How was your 2015? What goals have you set for 2016?

Quals incoming!

My qualifying exam is coming up, in a little over a month and a half.

The format is writing the research strategy of an R01, based on proposed research for the next few years, then presenting and defending the ideas to your committee. I've been working on mine almost daily since May, and it's changed dramatically as the direction of my project has shifted. It's been fun, interesting, challenging, and utterly terrifying.

Other students I talk to say this was one of the worst parts of their PhD, the lead up to quals. These same people say that in retrospect, it wasn't that bad, and they enjoyed the actual event, in a twisted sort of way.

I've been trying to get the last few bits of preliminary data, and it's not going well. I would have no problem with data that contradicted my hypothesis, if only the experiments would work. That frustration aside, the writing process has been enlightening. Reading papers, and putting this puzzle together has been satisfying in a way I hadn't expected. I don't mind the writing at all, but I'm dreading the studying that I should have already started. I'm also looking forward to dedicated time in the lab again, instead of random hail mary experiments.


How was your qualifying exam? Horrible? Wonderful? What do you wish you had done differently?

Onwards, and forwards!

Halfway Done! Revisiting 2015 Goals

June. It's June already. Where did 2015 go? Time is flying by at a ridiculous pace. In January I wrote a post about goals I wanted to achieve for 2015. Since 2015 is halfway over, let's revisit.

Professional:

• Publish in a policy journal again - Not even close, and maybe not something I want to focus on.
• Plan & execute DC networking trip - Went to DC, but not for this purpose. still managed to get some networking in.
• Identify & explore specific science policy careers - This is still a struggle
• Find session/panel to moderate at future conference - I'm going to a conference in October where I may look for future opportunities.
• Finish strategic outreach plan for CCH - Done! Interesting side project, glad it's over.
• Co-moderate PhD Career Conference 2015 - Currently in the final stages of setting up workshops, this event is at the end of June.

School:

• Submit F31 grant - Still writing, writing, writing. Submission deadline is in August.
• Pass qualifying exam - Committee is formed, this will be scheduled for September.
• Attend 2 conferences - Done! Going to a 3rd in October.
• First author scientific paper - Done! Submitted earlier this week, keep your fingers crossed that comments are kind, and revisions are light.
• Read at least 1 paper per week - Not quite. I've been scanning more abstracts, but need to focus on more indepth reading.

Fitness:

• 300lb deadlift - Not even close
• Gym at least 2x/week - Only for the last month or so. As this continues more of the other goals in this category will seem more attainable.
• 10 sec L-sit
• Freestanding handstand
• 5 pull-ups
  

Personal:

• Travel out of the country - Twice! Once for a conference, and once for fun.
• Complete Linux online course - Nope. This isn't a goal any more.
• Practice piano 3x/week - I don't think I've looked at my keyboard since January.
• Take singing/piano lessons - No longer a goal, but I might take lessons after I pass my Quals.
• Blog monthly - Obviously this hasn't been happening.
• Have more science-specific Twitter discussions - This has been happening periodically, and it's always enjoyable. 

Looking over the list, I'm pretty okay with my progress so far. Some goals have changed, and that's acceptable. I specifically didn't add goals to this list, but priorities have definitely shifted to focus on personal fitness, and my research project. In January, I was still in classes, and focusing on bigger picture, career orientated goals instead. This mid-year shift seems appropriate, and we'll have to see what I think looking back at the end of this year!

How are your goals coming along?

Science of Being Happy: Sleep

Building on a previous post about using basic needs as a coping mechanism, I am very interested in research on happiness. Considering some of the dark episodes I've had in my life, I get a little angry when people think my buoyant optimism comes naturally. Happiness can take effort and work, just like any other goal worth pursuing.

In the hierarchy of health, sleep is king. Like many other things in life, happiness starts with basic needs being met. It's much easier to be happy when you sleep well, eat well, and get a moderate amount of exercise. Specific needs may be different for different people. I need a fair amount of sleep, and boy howdy, everything in life is easier when I get it. Thinking is faster, and clearer, mood is better, and productivity soars.
But it takes more than going to bed at a regular hour (even though that's still important). Here are the things that work for me:

• Sticking to a schedule: We've all heard this, so why don't we stick to it? It's hard to implement, but it really does work. I get tired around the same time every night, and getting up during the week is far easier if I didn't sleep in all weekend.
• Get away from the screens: There's interesting research about the effects of light from computers and smart phones. The over-simplification is that the wavelength of light given off from these screens is similar to sunlight. This light stimulation is enough to stop all the night-time hormones from kicking in and helping you wind down for the night. Remember that we evolved to be in tune with sunlight, so by playing on the phone in bed the same as telling your body that it's daylight and not time to sleep yet. However, I'm in grad school and you might have a similar obligation that means turning off the computer hours before bed isn't an option. Instead, I got these super fashionable amber-colored glasses (About $15 in late fall of 2013):
  
  
  
  
  
  Yes, I look pretty fantastic there. Sex appeal aside, these things have been amazing. Supposedly, they block the wavelengths of light that keep you awake, and let your body send out all the sleepy-time signals. I noticed that I get drowsier earlier, and fall asleep faster.
  
• Daytime light exposure: The other side to this is getting enough light during the day. I work in a lab with no windows. During the winter it's usually dark when I'm walking in, and dark again when I'm walking home (yay, Northeast winters). This means that unless I make a conscious effort to go for a walk or get near a window during a break, I get zero light exposure. My sleep took a significant turn for the better when I started taking a 10 minute break in both the morning and afternoon to get near a window, and usually a brisk walk right after lunch. 
  

• Exercise: This is another obvious, but easy to forget item. Don't sit at a desk all day. Get up and move when you can. At least stretch once in a while if nothing else. Movement during the day always helps me sleep better at night. Even simple activities, like an afternoon walk, work well.
  

• Light while sleeping: I'm not 100% sold on this one, but experts that I generally trust say it's important. We live in a very electronic world. Clocks, phones, computers, TVs, etc all have little lights that are shining on us all night. Just for the fun of it, try covering them up or turning them all off. Every pinprick of light you can see from your bed and see how you sleep. I found some improvement.
  

• Light while waking: Once upon a time, in a land far way, I used to live somewhere that got sunlight. Waking up in the morning with a large, East-facing window was easy and felt natural. Now that I'm in the Northeast, if I waited for sunlight to wake up, I'd sleep until June. Instead, I invested in a sunrise alarm clock (about $80 in summer of 2013). This is the most expensive clock I ever bought, and it's been worth every penny. It gradually gets brighter during the 30 minutes before the alarm itself goes off, up to a final brightness that you set. The alarm is either wind chimes, or bird chirping. The gradual brightening of the room makes those gentle sounds enough to wake you up. Waking up in a brightly lit room to birds chirping is so much nicer than waking up to a pitch black room with an alarm beeping angrily at you. I can't recommend this thing enough.
  

So here are some of the things I do to make sure I'm well rested, at least some of the time. Like many of my ideas it works great in theory, but doesn't always get put into practice. However, when I'm starting to feel overtired or stressed out, sleep is one of the first things I try to focus on improving. I'd love to hear about what you tried, and what's worked and what hasn't.

Goals for 2015

Oh, you know. It's one of those posts.

I don't want to reflect too hard on 2014, because I had no idea what I was doing for most of it. With my personality, I'd rather look ahead. I'm halfway through my 2nd year of grad school, and here are my goals for 2015:

Professional:

• Publish in a policy journal again
• Plan & execute DC networking trip
• Identify & explore specific science policy careers
• Find session/panel to moderate at future conference
• Finish strategic outreach plan for CCH
• Co-moderate Career Conference 2015

School:

• Submit F31 grant
• Pass qualifying exam
• Attend 2 conferences
• First author scientific paper
• Read at least 1 paper per week

Fitness:

• 300lb deadlift
• Gym at least 2x/week
• 10 sec L-sit
• Freestanding handstand
• 5 pull-ups
  

Personal:

• Travel out of the country
• Complete Linux online course
• Practice piano 3x/week
• Take singing/piano lessons
• Blog monthly
• Have more science-specific Twitter discussions

A few notes:
I feel the need to separate Professional goals from School goals because even though I'm in a traditional research lab, my current career plans are aimed at science policy. About that 300lb deadlift: my max pull has been around 225-245lb since the very first time I tried over 5 years ago. I've been claiming 300lbs as a goal for a very long time. Time to stop screwing around and get at it. Some of the other goals seem a little lofty, but might as well think big, right?

What are your goals for the upcoming year?

Surviving an Academic Schedule

This is a guest blog post for PhDtalk as part of a series on academic schedules. I was asked for “a narrative about how a (normal) day/week in your life looks like, and how you combine research / writing / teaching (if any) and other activities on a regular basis, and how (or if) you manage to squeeze in some time for yourself as well.” Original post can be found here.

The President of the United States doesn't decide what to wear or eat every day. Humans have a limited capacity to make decisions. Once the quota is reached, there has to be a rest period before being able to make more decisions or it starts to feel physically draining. The POTUS spends his day making important, far-reaching decisions. There's no point in waste precious energy making small ones.

I keep this in mind when devising my daily and weekly schedules. Having a routine keeps my mind free for the things that matter, and still ensures that everything gets done. I optimized my morning routine by writing down everything I wanted to accomplish before leaving the house, then put those things in an order that made sense. A few key points: I don't look at my phone before getting out of bed. I'm a graduate student. No email is so important that it can't wait a few hours. Looking at my phone makes me laze about too long. Secondly, I do a small amount of physical activity as soon as I roll out of bed. This might be a few yoga poses or a set of pushups. Something short and fast to get blood flowing and let me body know I'm up.

Mornings are my golden time. I can get more quality work done before 9am than the rest of the day combined. I recently started harnessing this by going to school later. Once I'm ready for the day, I spend about an hour (7:30-8:30am) writing, or working on one of my side projects. If I go into the lab this early, there's almost always something to distract me. Staying home, I have a comfortable setup, with no one to interrupt me.

My morning hour of productivity is broken up by day. The night before when I'm setting my to-do list, I decide what will be the priority the next morning. It's usually one of the following:

• writing: blog post, homework, abstract, manuscript, whatever is in the pipeline
• policy work: I'm starting a student science policy group. This is when I research speakers, write emails, plan meetings, etc
• networking: send emails, research people I want to meet, career paths I'm considering, etc
• GSS: another student group I'm part of at school. During this time I plan events, write emails, read over meeting minutes
• reading/lit search: I have a never end list of papers I'm trying to read. I try to get through a few during this time.

These categories get attended to once a week, or less if nothing is needed. The default is always writing. Even if I have no deadlines, I always have a handful of blog posts or writing exercises I'm working on to improve my writing.

I live and die by my calendar and a master to-do list. I carry a notebook everywhere and continually jot down ideas, and things I need to do. I have 30 minutes blocked off at the end of each day where I go through that notebook and transfer things to my to-do list and calendar. I don't necessarily get to everything on my calendar, but if it's not on the calendar, then it definitely doesn't get done.

Let's start with the long-view and work backwards:

Five Year Plan
I have a five year plan. It's hilariously optimistic. I would like to graduate quickly. If there's any chance of that happening, there are many things needed to stay on track. These miles stones are set on this five year plan. They get reviewed and revised about once a month to make sure I'm not missing any big deadlines.

Monthly
Near the end of every month, I set goals for the upcoming month. I look at my five-year plan and my previous month's goals and think about what I need to accomplish to move forward. These might be academic (narrow topic for review article), social (host a dinner party), health-related (do 10 pushups every day) or something else entirely. I then set time aside in my calendar to accomplish these.

Weekly
Every Friday afternoon, I set my schedule for the following week. I look at my to-do list, and block time out for each item. To-do lists are great, but without setting aside actual time to finish things, I never seem to get around to them. This also gives me a chance to be aware of any upcoming meetings I need to prepare for, exams coming up, or similar obligations.

Daily
Before bed I review the next day's schedule. I change or prepare things as needed.

Everything I do goes on the calendar, including exercise, grocery shopping, cleaning, studying, and time with friends. I use one color for social activities, one for lab work, and one for school work. When I'm planning experiments in the lab, I block out time to prepare and set up, time to actually run the experiment, and time to analyze the data. I block out time for classwork, and time to review lectures. I even have a daily reminder to leave time for lunch every day.

I have a super-packed, color-coded, scheduled-to-the15-minute-increment calendar.

Here's an important note: My precise schedule doesn't always go as planned. I'm still horrible at estimating how much time something will take. However, I find it invaluable for making sure I get the important things done. It's hard to tell how much you've taken on until you start planning out the specifics. My calendar had been a valuable tool for letting me know when to say no to new obligations.

Sleep, nutrition, and exercise are all very high on my priority list. They might slip for a week before a deadline, but being healthy and happy are more important to me than anything else. My calendar helps me to not take on too much, and to lead a happy and productive life.

What a Difference a Day Makes

In September, I went on a whirlwind trip to Washington DC. I spent a day and a half in my nation's capitol, to visit Congressional offices and talk about the importance medical research. Almost 300 people were part of the Rally for Medical Research, all with the same message: Now is the time for Congress to come together and support the NIH with continued funding for medical research. We had training on how to deliver our message, and a reception with talks by Dr. Francis Collins and Senator Dick Durbin before being unleashed on Capitol Hill to attend our meetings. AAAS was kind enough to facilitate my involvement with this opportunity.

Thirty-six hours in DC, meetings in seven different offices, could that possibly make a difference? I've been asked many times since returning: Did you make a difference? As a graduate student, I have many, possibly naive ideas about making an impact and changing the world. I want help people live better, healthier lives, and leave the world in better shape than I found it. This might be through my own disease-curing research, or it might be by convincing one more member of Congress to sign a bill that supports NIH funding, thereby helping others with their own research.

As a researcher, I think about disease in a very specific way. I think about it mechanistically. I ponder why a mutation in one gene can throw off an entire system. I want to know how and why this happens. Patients with various medical problems also attended the Rally for Medical Research. They think about diseases differently. Patients and their families have to live with a disease. Interacting with someone who has survived a severe brain tumor pulls the science out of the Petri dish and puts it into a person. Interacting with patients and survivors is a stark reminder of the ultimate goal of medical research – to help people. These patients, along with patient advocates, and other researchers were part of our group that spent the day talking to members of Congress about how continued NIH funding is needed.

But can one day of conversations change anything? We spoke with the decision-makers who seem far away, but who directly impact our lives. Our government is made up of individuals, making individual decisions. As a voter, it is my right and my responsibility to let them know which decisions are important to me. One conversation may not change anyone's mind. However, each conversation is part of a larger movement. A small, steady voice can have as much impact as a single loud one. I view this trip as part of a continuing message, and not a single event.

This is why advocacy is important. Legislators have to take into account the views of many constituents. If one group don't speak up about an issue that matters to them, a different group will. The onus is on the voter to let their views be known. Washington DC is a fast-paced town, and issues can quickly be forgotten. We need to remind Congress which issues matter to us.

So did a day make a difference? It did for me, and I hope it does for the future of funding for medical research.

What would you want from a SciComm class?

In the Spring of 2014 I took a class that was required for my program: Workshop on Scientific Communication. While not knowing entirely what to expect, I was still a little disappointed in the content. This one credit, twelve session class was mostly long, text-heavy PowerPoint presentations on how to write papers, what the purpose of an abstract was, how to prepare figures, and similar topics. While these are useful topics, there seemed a lot missing from the class. Many slides were read to us on how to write an abstract, but we never actually wrote an abstract. We were required to do a ten minute oral presentation near the end of the semester, and received some valuable feedback. However, we never got a chance to revise and improve.

I approached the instructor, and asked to TA next time the class was offered. She said the class was a lot of time and effort, and she would love the help. I asked about including some extra topics, and got a very enthusiastic response.

Here are some things I would like to see added:

• Twitter: what it is, and why it can be useful
• Blogs: how they can improve writing
• Science policy: what is it and the importance of communication and advocacy
• Scientists speaking to the lay public: how to do this and why it matters
• More opportunity for feedback: we're often told the importance of good writing, but don't to practice.

And now I open it to you. What would you want to learn from a graduate level class on science communication? What do you wish other people would learn? This class is generally geared toward graduate students, but also attracts medical students, residents, and other people from the medical campus that were intrigued by the title.

What are your thoughts?

What I Study

In my Careers in Scientific Communications class, we were given the writing assignment below. I liked it enough to post my answer here. I would love to see yours too!

Write a short essay (125-175 words) about your lab research or a science topic of your choice. The essay should describe/explain the science so that it is understandable to the non-scientific public.

I study how stem cells make and use energy - stem cell metabolism. I don't use the controversial stem cells that get all the headlines. Instead, I use stem cells from bone marrow, also called mesenchymal stem cells or MSCs. Stem cells have two defining properties that make them stem cells. First, they can make more stem cells, exact replicas of themselves. Secondly, a stem cell has the ability to become a different type of cell. MSCs can become bone, fat, or cartilage. There are two main ways cells make energy. Glycolysis makes a little energy, and doesn't require oxygen. Oxidative phosphorylation does require oxygen, and makes a lot of energy. Stem cells mostly use glycolysis. Bone cells mostly use oxidative phosphorylation. Somewhere along the path from stem cell to bone, the cells switch how they make their energy. If you stop oxidative phosphorylation from happening, you also stop the stem cell from becoming bone. We don't know why or how this switch happens, and that's what I want to find out.

Writing Exercise Turned Publication

I have a writing group. It is awesome. We meet once a month. The day before we meet, we send each other some writing we've been working on. One page limit. We then meet for an hour, and tear apart each piece. It has both improved my writing, and inspired me to write more.

About a week before our June meeting, I was casting about looking for something to write. I had no upcoming abstracts, no manuscripts in process, and no blog posts in the pipeline. Then I got an email from a new student journal that I read about science policy, the Journal of Science Policy & Governance. It was a call for submissions for their upcoming special edition on Healthy Food Policy.

I'm interested in science policy. I think it would look good on my CV to publish in a policy journal. My writing group was in one week, and the submission deadline was the following day.

Challenge accepted.

I spent some time thinking hard about topics, then a week of literature searching and mad writing. Submitted, and to my surprise: accepted.

The editorial team at JSPG is really fantastic. They helped to really polish the piece, and give it better flow. This also helped me realize the importance of writing regularly. Publishing was a bonus, but achieving the goal of actually finishing it was incredibly satisfying.

The article is linked below, and any comments are always appreciated.

http://www.sciencepolicyjournal.org/special-edition-healthy-food-policy.html

Science of Being Happy: Back to Basics as a Coping Mechanism

Life getting to be too much? It was for me. Through the winter of 2012 into 2013, everyday functions were becoming a problem. Getting out of bed, getting to work, and taking care of myself all became insurmountable tasks. I'll spare you the details, but eventually, with time and the help of some wonderful people, I got into a better place.

Every now and then, the darkness comes knock, knock, knocking again; when I haven't slept well in days, when stress from grad school get overwhelming. There is one thought exercise that pulls me away from that abyss almost without fail.

"I have a roof overhead, and food in the belly. Everything else is a luxury."

I return to the absolute basics of survival, and start a list in my head of how they all get met without fail in my life. I know where I'm sleeping tonight. I know where my next meal is coming from. If the plans I have in place for each of those were to fall through, I have other options.

Using Maslow's hierarchy of needs, we can expand: there's no one trying to kill me. My personal safety is not in imminent danger. I have a job (more or less). I have no major health issues. I have family and friends I can turn to in times of need. I could go on, but you probably get the idea. I often don't even need to go through the whole shebang, but just the first line a few times:

"I have a roof overhead, and food in the belly. Everything else is a luxury."

It sounds too simple to work, but it works for me. This has become incredibly useful in dealing with the stress of grad school. When I remember that all my basic needs in life are more than adequately met, it seems like less of a deal that I have an upcoming exam that I'm not prepared for, that my schedule is packed, that day to day life is stressful.

This might be too dark for some people, but I find it comforting. If I were to fail out of grad school, if the PI kicked me out of the lab, if I had a major medical emergency, everything would still be okay. Because I would still have a roof over my head, and I would still have food in my belly. And everything else can be dealt with. 

It's Been Said Before, Just Not By Me: Discussions on Open Access

Open access is a big buzzword in the world of science these days. One Friday morning, I decided it was time to learn a little more. The idea of open access gets tossed around a lot, and it sounds good in theory, but truth be told I know little about it. What do I do when I need information? I tweet about it:

My followers (affectionately referred to as my Tweeple, or my Tweeps), have proven to be a valuable source of information with a diverse range of opinions. The first response was from a fellow graduate student:

Flippant at first glance, until further pondered. I was between institutions during most of the summer of 2013, after leaving a job as a technician, and before starting grad school. I was unaffiliated with a university, but still interested in science, and wanted to keep up with new research. There are sources for "science news" (Live Science, The Scientist, Scientific American, to name a few), but if I've learned anything about scientific communication (#scicomm), it's to check the original reference before getting too excited about a new discovery. Unfortunately, I wasn't able to do this. I was surprised at just how often I was attempting to get papers I didn't have access to. Open access is more than not needing a library, but also being able to keep up with new discoveries and keeping current with the disciplines that are important to me. As I found out that summer, you can't do this without institutional access. 

My response (mostly playing devil's advocate), was that if the next generation of scientists all chose to publish open access, then the status quo would shift and the change would happen naturally.

We had a fairly predictable back and forth about needing high impact factor for grant funding, and discussing whether impact factor is really all that relevant. Some scientists, physicists in particular, seem to favor h-index, calculated by citations per published paper. It is the opinion of this barely-published not-quite-scientist that individual citations matter more than a journal's impact factor because impact changes year to year, but citations are the timeline of science.

From there, we had a different viewpoint chime in. a PI responding to the question of what open access means to him: 

He went on to remind me that he already pays overhead costs to a library that covers subscription fees, and that cost to him wouldn't go away if he published all his papers in open access. Despite his reluctance to the currently proposed model of open access, he still agrees that the public should be able to access the results of the research they fund through their taxes. But this model isn't going to get changed by people who have no incentive to change it.

Then I was asked the big question:

I'm stumped. It's one thing for rock stars like Randy Schekman to decry the luxury journals right after winning a Nobel Prize. But if I had a paper, as a graduate student, that was capable of getting published in one of the big names, would I turn down that career-boosting opportunity for a model that I think is "a pretty good idea, at least in theory?"

Should these changes be coming from top-tier scientists who already have a reputation and little to lose, or should the next generation give up the old ways and blaze a new trail?

Luckily (or unfortunately), I don't have to answer that question yet. However, I do think it's important for people even at my early career stage to be thinking about these topics. I'm part of the next generation of scientists, and if we don't think about what needs to be changed, who will?

Science for My Mother

I'm a scientist and science lover. Undergraduate researcher to technician/lab manager to graduate student. My mother is not a scientist. She hasn't taken a basic science class in over 30 years. My mother is not stupid. Despite what I thought during my teen years, she's actually quite intelligent. She reads books, newspapers, and websites, working to stay educated and aware of the world around her.

You can imagine my surprise when I learned that my mother had never gotten a flu shot and thought that they are a bad idea. I asked her why she thought they were a bad idea.

"Because they're injecting you with something."
"Because I rarely get sick and would be really mad if I got the flu from one."

I asked her if she knew what was actually in the flu shot. She said no.
I asked her if she knew why the shots were given. She said no.
I ask her if she wanted to know. And she said of course.

We went on to have a conversation about the immune system. About innate and adaptive immunity. About memory cells. About what is actually in the syringe. I was auditing an immunology course at the time, so I was reveling at getting to use all my newfound knowledge. My mother has almost no biology background on which to hang these facts, so it was a thirty-thousand-foot overview. She kept asking questions, about how things worked and why people were against receiving the shots.

By the end of the conversation, I hadn't convinced her to get her flu shot - which is fine, that wasn't the goal. But now she has a more informed opinion. She has more information to think about and is basing her actions on facts rather than attention-grabbing headlines.

That's good enough for me, and that's why science communication matters.

March 10th, 2014 Update: Mama finally stumbled across this blog. Turns out she did end up getting a flu shot :)

The Bugs Controlling You

There are between 300 and 1000 different species of in your gut, totalling over 100 trillion microorganisms. There are between 5 and 50 trillion cells in the human body. That means there are more of them than there are of you. Creeped out?


To some, bacteria is a bad thing. This is why antibacterial soaps and hand cleansers are a multi-billion dollar industry, predicted to reach over $40 billion by 2016. However, people are starting to understand just how vital those microscopic bugs are for our existence. Take your gut, for example, your GI tract, the poop-shoot, that single long tube that turns food to fertilizer (Disclaimer: human feces is not a good fertilizer). There's bacteria in the biofilms of the mouth, bacteria in the stomach and perhaps most importantly, bacteria in the small and large intestine that help digest carbohydrates and absorb fatty acids. This same gut microbiome is increasingly thought to directly influence brain function as well. That's gut bacteria, playing a role in your personality.

You can't function without them because they protect you. They help digest your food. They produce amino acids that you can't survive without. There is plenty of research that shows just how integrated you are with your little friends. The health of the gut microbiome is being linked to obesity, bone health, immune function and mental health. And this is no longer new and surprising (to most people). The scientific community at large has accepted the fact that we are covered inside and out with some extra friends that we heavily rely on. 

So why are people so resistant to new research showing that a parasite from cat intestines may be controlling our brains?

Wait. What?

A handful of studies on Toxoplasma gondii, (all linked from this article, which what got my attention in the first place) have shown some personality quirks that are far more prevalent in those tested for the parasite. These individuals are more likely to be uncoordinated enough to have more car accidents, less likely to seek out new experiences, and they show a higher correlation with schizophrenia. Unlike your gut-dwelling friends, there seems to be little positive outcome from contracting T. gondii.

The research of one of the experts in this area, Jaroslav Flegr, hadn't been taken seriously by many for a good portion of his career. People are resistant to the idea of parasites controlling their personality to such a degree.

However, upon further reflection, it doesn't seem that unlikely. If there are bugs controlling so many aspects of our physiology, from weight to mood, why wouldn't they have an affect on personality too? As uncomfortable as it is to ponder, as time goes on, it wouldn't be surprising if we discover even more of "them" controlling us. It's just one more reminder that humans are inextricably linked to the world around us.

 

Finding Science

School is hard and life is expensive. I worked throughout my undergraduate degree to take out fewer loans. Eventually I decided to quit my full-time job to focus on school; I was looking for work relevant to my degree in Biological Sciences. On a whim, I applied for and was awarded a summer fellowship to do research in a cell biology lab. I had no idea what research was like and had taken few classes within my major. I just needed some money and something to do with my summer. 

My first day in the lab, the PI explained the project I was joining: cells that appeared to change morphology when a certain receptor was stimulated for an hour.

“An hour?” I said, “What happens to them after an hour?”

Her response floored me: “I don't know. That can be your project.”

She didn't know? But she’s a professor! I thought scientists knew everything. Can’t we Google it? Look it up in a textbook? Ask someone else?

It wasn't until later that I began to understand. The answer wasn't out there, because no one had ever asked that specific question. Research is about exploring puzzles that have yet to be solved. Instead of asking someone or finding the answer in a book, you have to figure it out. From that epiphany on, I got hooked.

That was 5 years ago. The shift in thinking that research fosters is amazing. It's a little X-files-ish. Now I question everything. Trust no one! (at least not until you see their data). I want to know how things work. I want to know the whys, the hows and most importantly, the mechanisms. Don't tell me that eating XYZ is healthy unless you can tell me what exactly its doing and why. 

Science has turned me a little pedantic, but it has opened up a whole new realm of humor as well:

If you have a mol of moles, digging a mol of holes, what do you see?

A mol of molasses (mole-asses). 

At any rate. Science is awesome. I'm making the transition from lab technician/manager to graduate student this fall. 

I can't wait. 

The Birth: What the Heck is Twitter?

Welcome to Shum Stuff. Or if you want to re-punctuate, you could also consider Shum's Tuff. I'm pretty okay with either one. I'm a Shum, one of many. This is my stuff.

Let's get one thing straight from the beginning. Shum. It's pronounced exactly as it is spelled. Shhhhhh. Ummmmm. Put it together now: Shhhuuuuuuum. As you can tell, it's a bit of a pet-peeve to have my last name mispronounced. I could understand if it had multiple vowels, or at least two syllables, but it's about as simple as it gets. Shum. Rhymes with bum, dumb, thumb, and scum. If you can come up with a nickname I haven't heard before, you win a prize! A small, cheap, probably plastic prize. Possibly a pipe cleaner.

Moving on.

Not too long ago, I could not for-the-love-of-all-that's-holy figure out what the big deal was about Twitter. I had an account. I had followed about 10 people, and had about that many following me (lookout behind you!). I would log on about once a month, look around a little and not really get it. I'm a scientist (or pretend to be), so I don't really like it when I don't understand things. It was time to figure out why people tweet.

As any reasonable 21st century woman does when she wants to embark on a new adventure, I Googled it. The best advice I found was to be active. Tweet, respond, follow, jump into conversations. Unless you're a celebrity, people won't come to you. You need to engage them.

And so I did. I started tweeting something 2-3 times a day, whether it be retweeting, responding to a question or just plowing my way into someone else's conversation. But the real trouble started when I followed @JacquelynGill. If you are unfamiliar with this ecologist, biogeographer and twitter-fiend, check out her blog here. I retweeted a few articles she wrote and it started a conversation. People in her science-sphere saw our conversation and followed me. I did the polite thing and followed them back. 

Then things started to snowball. You see, the fascinating Dr Gill is heavily into science communication (#scicomm). Science communication is exactly what it sounds like. Communicating about science. This can be between scientists, journalists, the general public or combination thereof. Science research, science policy, science education. These people are obsessed with science and attempting to engage those around in conversations. It just so happens that they were all at a convention about science communication, causing them to really blow up the Twitter-verse.

By golly, I had no idea that this was a topic so fascinating. As a lab technician, I talk a lot of science every day. The few non-scientists I interact with on a regular basis know a-plenty about science by sheer virtue of interaction with moi. In this insular science-drenched world it's easy to forgot that a shocking number of people still discount global warming, evolution, or even the basic science needed to make educated opinions about their own health care.

Science communication is vastly important, and I'm hooked on being a part of it. Where is my place in all this? I don't know yet. Stay with me to find out.

I'm a Shum, and this is my stuff.