A Grad School Gardener

I wrote this on the plane while thinking about an upcoming GotScience Magazine series that will explore urban gardening. This story doesn’t exactly fit the science-focused mission of my blog or the GotScience series. But this is a story ultimately about my Mom, who inspired this blog and my desire to garden. 

My parents had a huge garden in our sprawling New England backyard where I grew up.  My mom came from a long line of farmers, so gardening was “in her bones,” even if it wasn’t in her children’s. My sister and I complained every time we were asked to go pick the green beans, zucchini, strawberries, tomatoes, lettuce, cucumbers, snap peas, and whatever else had ripened overnight. But firmly rooted in my memory is the taste of a tomato plucked off the vine and popped directly into my mouth or the crunch of the baby carrot cleaned off with the dew on the grass. It may be these memories that, despite our resistance to gardening, led both my sister and I to plant gardens the second that we had the opportunity.

My opportunity was in graduate school.  Living in a small set of six rooms on “The Farm,” I could look out my window and see the rows of corn grown for genetic experiments. This corn grew out of Barbara McClintock’s pioneering work in understanding transposons (also called “jumping genes”) that led to her Nobel Prize in Physiology or Medicine in 1983. But right next to the corn field was a smaller field commandeered by another graduate student whose goal was to grow an award winning giant pumpkin.

The fields that were offered to the students and faculty at Cold Spring Harbor weren’t nearly as well-controlled as those at The Farm. Originally, the set of 10×10 foot plots were tucked away in the middle of a wooded area that was a short walk or drive from campus.  The only rule was that you couldn’t grow corn  – because we couldn’t risk it pollinating the experimental corn and ruining the genetic experiments.

My first grad school garden in the woods

When you give a bunch of scientists land, they tend to till it with the focus and academic rigor that they bring to the hours and hours of laboratory work. These gardens were experimental, but not in the traditional sense. I experimented with growing different vegetables – beets and heirloom tomatoes – than what my mother grew. I also tried different weed suppression techniques, in part to avoid pesticides but more to avoid the tedious (and time consuming) task of weeding. Straw was highly effective, but only if put on the beds before lots of weeds started to grow. The negatives – made a mess in the car.

The next summer, the gardens were moved out of the forest and on to a hill overlooking the volleyball courts. There was a fierce volleyball competition amongst over a dozen scientist-filled teams each summer, so this locale was convenient for garden tending post game. The garden community thrived here. It was so popular that people started to share their small plots along with their advice and vegetables. Within a small research institute on Long Island, it pulled the scientists out of the labs, into the sun, and as a side effect, put tons of fabulous food on our tables each summer.

I look back fondly on those days. Since moving to Phoenix, I haven’t yet mastered the art of urban (and desert) gardening. But I now understand why my mother toiled each spring to prepare a garden to harvest all summer. There’s something about having your hands in the dirt and crunching into that first carrot of the season that you grew yourself that makes all the work worth it.

 

 

 

 

Why I March: March for Science

The March for Science is this Saturday April 22nd. Thousands (perhaps hundreds of thousands) of scientists and supporters of science will take to the streets in Washington DC and over 517 cities in satellite marches around the globe. I will be marching virtually from my sister’s home in Bend, Oregon.

Why do I march? I march because science is incredible. How cool is it that some people have DNA from two different people in them? How cool is it that scientists are working on curing HIV/AIDS with cord blood transplants? How cool is it that science has increased the length and quality of our lives, in part by eradicating childhood diseases like polio?

My goal as as a scientist is to help scientists do what they do best: research. Research can only be done by funding and supporting science.  Since much of scientific funding comes from the National Institutes of Health and other government agencies, we need to make sure that this support of science continues to be a nonpartisan priority. We need to support our young scientists so that a generation of science isn’t lost.

My goal as a human (who happens to be a scientist) is to empower the public. I want to help the public understand science and health, but I also want everyone to know (or feel like they know) a scientist. It’s a tough road to slog when people don’t trust in science. A first step in fixing this may be making sure that every single American knows a scientist. A recent survey found that people are more likely to trust news from a Facebook friend. Wouldn’t it be great if everyone had a scientist as a Facebook friend?

So I march for science. I march for progress. I march for our present. I march for our future. And I march for all of you, since I am your Facebook science friend.

Persuading the Unpersuaded

I haven’t blogged for a while. I had a baby. Babies take up a lot of time and energy. Lack of sleep doesn’t make for good blogging.

But I also got discouraged.  This election and the potential impact it will have on science and health is discouraging.  The shouting of “fake news” from all corners of leadership because facts that they don’t like are being talked about is discouraging. (See a great video of Don Lemon walking off of the CNN set from real news being accused of being fake). My deep desire to share with you my passion for science but feeling like I need to address this political atmosphere (and really not wanting to because that’s not my passion and purpose) is discouraging.

But I’m a positive person. And as a positive person, I want to find a solution so that I can move forward and continue to do what I love to do – connecting science with the public.  So part  of my solution will be to stand will all people who support science and truth by participating in the March for Science on April 22nd here in Phoenix.

The other part of the solution will be harder.  I realized that not everyone knows a scientist. And maybe they don’t trust science and scientists because they have misconceptions of who we are and what we do. How can I persuade the unpersuaded and reach beyond the science bubble (as described in a recent Nature article)? I want EVERYONE to know a scientist, and I’ve realized it needs to start with me.

Stay tuned for more about this…but in the meantime, I will be blogging more in order to share with you all the awesomeness of science!!

Adding the “Art” to STEM

Science, Technology, Engineering and Math = STEM, add “ART” and you get STEAM.

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Cyndi and I in front of some cells

Friday night, I collaborated with my fabulous friend Cyndi Coon for a “STEAM-Y” Ladies night out at Tempe Center for the Arts. Scientists aren’t known for their artistic abilities, but Cyndi has the knack for drawing out the artist in everyone – even me, who insists I’m not a “draw-er.”  The whole evening revolved around creating your own “cell-fie.”

Bringing on the STEM

As the science nerd that I am, I was excited to talk about the connection between how cells look and how they function. In the examples below, you can see how lung cells have little wavy fingers called cilia that are used to remove debris from the lung.  Plant cells have a hard exterior cell wall, which help make plant’s leaves rigid.  They are also green because of the chloroplasts that harness sunlight and turn it into plant energy.  And in the breast, you can see that the cells are organized in such a way that an empty space (called a lumen) is created where breast milk is stored after pregnancy. There are so many cool examples! Pollen. Neurons. Blood cells. The list goes on and on!

What cells look like and how they’re arranged often help to understand how to cell functions

Adding the “A”

Cyndi brought the “STEAM” by talking about Ernst Haeckel who was a PhD trained zoologist turned artist. His illustrations are stunning! Many of his ideas about evolution and biology were later disproved, and he used creative license with many of his “subjects.” However, his art captured a Victorian audience. He was a true scientific communicator (or as Cyndi would say “performance artist”.

It’s from these dual inspirationsIMG_0360 that the thirty or so attendees got to work with their black paper, gel pens, and colored pencils. We were reminded that patterns often occur in nature as does some level of symmetry, which could be used to help us draw our cells. Patterns can be created by grouping shapes together, mimicking groupings of cells. Or you could draw cells so that you can tell from what they look like what the cell might do.

The group was so creative! You can be creative too! Take inspiration from this idea. Why not have your kids or your friends (with a glass of wine) create cellfies? And if you do, share them with me!

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I can’t encourage you enough to check out Cyndi’s creative work at Laboratory 5 or her speaker page. I love that her transformational talk will encourage you to “channel your naughtiness to expose creativity and use it as a super tool.” 

Read a version of this article with even more info about Ernst Haeckel at GotScience.org

What’s one thing that people don’t know about your job, but should?

On Facebook the other day, a post come up with answers to this question: what’s one thing that people don’t know about your job, but should?  I wish I could share the link, but I just can’t seem to find it. Perhaps this means that my answer to this question should be “Even though I’m a researcher, I can’t find everything I’m looking for by Google searching either.”

Joking aside, I have spent the last several days thinking about this question and what the answer is for me.  I’ve also asked my husband who is a Neuro ICU nurse and everyone else I’ve come into contact recently. For the record, the hubby’s response was that even though you only have two patients that you pay attention to for your 12 hour shift, they take up all your time and you barely have time to sit, eat or do anything else. (He’s such an awesome nurse!!)

Me - my first day as a newly minted PhD scientist!

Me – my first day as a newly minted PhD scientist!

I keep changing my answer the more I think about it. In part, this blog tries to demystify what being a scientist is all about.  I think I tell you about things all the time that you probably didn’t know about, like what a scientific meeting is like, how does the grad school experience work, and what in the world I do at an Institutional Review Board meeting. Also, as a scientist, I think one of the main things I want people to know about the profession as a whole is that scientists aren’t just one type or stereotype. Scientists can be nerds, we can work in the lab, but we are also in business, policy, the arts (and be nerdy or not – it all depends!).  We also have hobbies outside of the lab. I play in a handbell choir and love to bike ride bar hop. Friends of mine have hobbies as diverse as raising carnivorous plants, riding horses, or long-distance biking.  We’re just people too!!

But what if I had to choose JUST ONE thing about MY JOB that I’d want people to know. I think it would be the critical importance of communication. I spend the majority of the day communicating my thoughts and vision to my team, to my leadership, and to other people who will help my team achieve our goals.  I write papers and grants with the goal of communicating to reviewers, other researchers and funders the importance of my work. I communicate with people throughout the hospital asking questions, solving problems and working together to achieve our shared goals.

I know that communication is an important part of many (most?) jobs, but perhaps it is a bit surprising to non-scientist that it is so necessary for a scientist.  Maybe what I really mean is that so much of what I do every day, I can’t do on my own.  I rely on so many other people. Science isn’t a solitary as you might think!!

Then again, in 10 minutes I may think of something that I would want to people to know about my job EVEN MORE. Fortunately, I have this blog, and I can tell you all about it then – and I will.

What about you? What is your job and something that people don’t know about your job but should?  Share in the comments!

The Reproducibility Problem in Research

recipe

Image credit Pixabay

When you’re baking a cake, you follow a recipe that uses specific ingredients, added in a particular order, mixed in a specific way, and baked for a certain time at an exact temperature. But what if you made the cake twice?  Or three times? Will it be the same each time? Will your cake be “reproducible”? What if your baking powder is old?  The cake might not rise as much as normal.  Or you buy a different brand of flour? What if you’re baking at your sister’s house in Oregon at a higher elevation than normal?  Do you change the time or temperature that the cake bakes? How much? And what if you’re using your Grandmother’s handwritten recipe for her famous spice cake?  It’s filled with phrases such as a “pinch” of cinnamon or “about” 3 cups of flour.  Do you think it will taste the same as when your Grandmother makes it?  And what if two people try to make the same cake? On the Great British Baking Show, one of the challenges each week has each contestant follow the same recipe with the same ingredients to make the same baked item.  They NEVER come out the same because there is variability built until every step, even with the same instructions, equipment, and ingredients.

Science is sometimes a lot like baking.  Instead of a recipe, scientists’ follow a protocol (or standard operating procedure – shortened to “SOP” because scientists like acronyms). We purchase or make ingredients, typically called “reagents.”  Often a single reagent can be bought from many different companies or made in the lab by you or maybe by a technician, or maybe you were in a rush and you borrowed some from someone down the hall. In biology, biological materials like cells or enzymes are often involved.  These could be new or old.  You could have tested and “validated” your cells or antibodies or you could have relied on someone telling you that they are okay. Once you have all of your reagents pulled together, you do the experiment.

Experiments are funny little things.  You follow your SOP, but maybe one day, the 5 minute incubation turns into 10 because you were in the middle of answering an email.  Maybe another day you’re in a rush to get to a seminar so you skip a step.  Or maybe you’re training a new undergraduate how to do the experiment and you let them do a few steps on their own.

This variability is part of the reason why scientists repeat their experiments multiple times. Three, as you may expect, is often the magic number.  These data are then presented (for example, in a grant or a paper) either as a representative experiment, where only one of the three or more experiments are shown, or as an average of the experiments with “error bars” that often show how much the data differed between experiments.  This type of careful presentation gives other researchers more confidence that the result is real, as opposed to something that happened just because the new grad student messed something up.

The Reproducibility “Problem”

However, even with all this careful planning, there is a lot of chatter these days about the failure of scientists to be able to reproduce experiments.  One of the earliest papers about this topic came from researchers at Amgen who found that they couldn’t reproduce 47 out of 53 studies from cancer research labs. This has led to a snowball of studies and reports of the failure to reproduce data from various fields including biology and psychology. The most recent is a Nature Article surveying 1,500 scientists about their  ability to reproduce their own and others’ results in their own labs. 52% of these scientists felt that there was a reproducibility “crisis” and words like “bleak” and “discomfiting” were thrown around to express the severity of the problem.

So is there really a problem? Lots of papers have discussed this already, but I figured why not add my own opinion to the mix.  In part, yes, these likely is a bit of a problem.  This problem stems from using reagents you aren’t sure of.  For example, imagine that you think you’re studying prostate cancer and you think you’re using a cell line from a prostate cancer patient, but actually you’re using a super common cervical cell line? It happens all the time! An effort to make publishers and grantors enforce cell line authentication and other types of reagent confirmation before beginning experiments is gaining steam.  Not a bad idea and not too expensive.

Image credit Pixabay

Image credit Pixabay

Other efforts are also underway where a third party can be “hired” to authenticate results such as the Reproducibility Project. This is expensive, and time consuming, and one might wonder where the value lies in having someone else repeat your experiments? The value lies in having confidence in the result…but as we’ve discussed here already, the minute you move your experiment to another lab with new reagents and new people, you add more variability. If the experiment fails, how do you know it’s because the result was wrong or because someone else did it wrong?

This is where the issue lies, and I think it all comes back to the central goal of science and scientists. Scientists want to uncover what’s really happening in nature. Every experiment is done to test a hypothesis, and these results lead to more experiments and on and on. Even if an experiment doesn’t get identical results each time or can’t be reproduced in another lab, the fundamental question is whether or not the biological hypothesis is correct or not.  No matter what, scientists should always do multiple different kinds of experiments and follow-up experiments to confirm or refute their hypothesis. This all assumes that scientists are ethical and follow the scientific method – as opposed to folks who publish fabricated or modified data just to get a paper published (but that’s a topic for a whole other post!!)

So I guess the question may not be whether or not an experiment is reproducible, but whether or not the hypothesis is true. And if scientists focus on THAT as opposed to reproducibility, per se, then I think science is moving forward in a productive direction!

 

What does the “typical” career of a scientist look like

I kind of hate this title. It’s horribly discouraging for young scientists to assume that there is a “typical” career path.  However, over the past 50 years or so, there has been an “expected” path for all “real” scientists to take.  All of the quotation marks are implying that this isn’t the case – it hasn’t really been the case for the past 50 years and it certainly isn’t the case now.  But there was an expectation from the senior scientists and colleagues surrounding you that this is the path to take. (note: this is coming from the point of view of a biology PhD, which I have experience with.  This may be entirely different for other science degrees like math or engineering)

You start with graduate school. Three to six (or seven or eight or nine or ten!!) years of working in a laboratory and writing a thesis.  Hopefully along the way, you’ve written a few grants and peer-reviewed publications.  You’ve networked with colleagues in your field and found great mentors that have helped you along the way.  Before the thesis has even been written and defended, you take all of this hard work, and wrap it up into a curriculum vitae to send to principal investigators (also referred to as a PI) of laboratories that you might be interested in working in as a postdoctoral fellow (also called a post doc). If the PI has space (meaning funding) and is interested in your work, they may invite you to interview. During the interview, you will give an hour long presentation of your PhD work and the rest of the day will be spent with the PI and others in his/her laboratory talking about what they do, how they do it and whether or not you’re a good fit for the lab.  Most PhD graduates go on multiple post doc interviews.  I went on three before I realized that I didn’t want to do a postdoc.

Once you are offered a postdoc, you usually move to a new state and a new institution. There is a stigma that doing a postdoc at the same place that you do you PhD, even if it’s in a different lab, will not provide you with a varied enough research experience.  You are encouraged as a postdoc (and as a scientist, in general) to be okay with moving around. If you’re married, you and your spouse have to figure it out. Have kids?  Same deal.

So what do you do as a postdoc?  You do research in a laboratory, but with more independence than a graduate student.  You are often responsible for writing grants and supervising undergraduate and graduate students.  You are expected to work just as hard – nights, weekends, whatever it takes.  And now, your goal isn’t to graduate, but rather to get enough publications in high profile journals that you can get a faculty position.

How hard can this be?  There have been a lot of articles on this topic, so I won’t rehash here (you can read more in a recent Nature article about the “Future of the Postdoc“) except to say that there are more postdocs than there are faculty positions – BY A LOT. So you really have to stand out. Plus, you have incentive to get a faculty position because postdocs are not paid very well – the NIH salary cap for first year postdocs is $47,000.  Keeping in mind that this is not a 9-5 job, but usually a 60+ hour per week job.

How do you know you’ve completed a postdoc? You don’t.  You either feel like you can start applying for faculty positions or not.  If not, you may want to do a second postdoc.  It’s not uncommon for people to do two 4-6 year postdocs before applying for faculty positions.

Now, I don’t have personal experience applying for faculty positions, but I have many friends who do.  The process of applying is like applying for many other types of jobs except there is an application “season” so that acceptances will come out in advance of a new academic year. Of my friends who have applied for faculty positions, the fewest jobs someone has applied for is about a dozen, but it’s not unheard of to apply for 40 or 50 positions with the hope of getting a handful of interviews.

Because this is so competitive, location is only a passing consideration. You may love Florida, but you’re moving to Minnesota if the best job offer is there. There’s also this fascinating phenomenon in science called the “two body” problem (see more in an interesting Scientific American article). This is when both partners are scientists and looking for jobs in the same place at the same time.  It’s an incredible challenge, and I know many people who have lived in different states from their partner for months to many, many years.

Although a faculty position isn’t the end of a journey – there still tenure, inventing something and start a company, moving to a new institution and all the other ups and downs that come with a job – this is the “typical” goal of many scientists. And it’s a wonderful goal.  It’s a hard road to tread, but without dedicated researchers willing to take the time and sacrifice needed to get to this point, there would be far less scientific innovation and discovery happening in the US.

On a personal note, when I was in graduate school, I distinctly remember a conversation I had with an unofficial academic mentor (thank you Bill Tansey for being so supportive all those years). I was getting close to graduating and he asked me what I wanted to do when I graduated, since he expected that I was applying for postdocs with the goal of becoming a faculty research scientist. I hadn’t once considered taking this typical career path (you can read more about my journey here). But I remember feeling proud that he thought that I could. It actually made me realize that even though I wanted to take a different path, that it wasn’t from lack of intelligence or academic ability. It’s just that we all take our own path, and mine wasn’t going to be “typical.”

 

 

 

What’s been going on?

It’s been a while since I’ve been able to blog.  I have lots of reasons, but one of the big ones is that I’ve been writing and editing for some other sites!

In mid-January, I wrote an article for the ISBER News Blog (ISBER stands for the International Society for Biological and Environmental Repositories – the premiere biobanking society in the world). The article entitled “Have you joined the ISBER social network? Facebook!” is all about how to get started on Facebook and how to get more involved with ISBER through that social media outlet.  If you aren’t on Facebook already, you may find the first half of the article useful.  Once you join, you can follow the “Things I Tell My Mom” Facebook page where I post often about interesting science I find around the web.

From this experience, I was named the new Assistant Editor for the ISBER News Blog. This was announced in a very funny article from the current editor Rick Michels called “Bringing in Backup.” I’m super excited about this new role and have jumped right in to help edit lots of interesting articles from the biobanking world.  I hope many of them will be interesting to the public, and I’ll be sure to share them either through this blog or on my Facebook page.

As part of my job, I endeavor to educate the public on the importance of biobanking in enabling cancer research. To both work towards this goal as well as to talk about the Biobank’s support of World Cancer Day, I wrote an article for the Barrow Neurological Institute blog about what our Biobank does to help cancer research. You can find that article here.

And because that’s not nearly enough, my first article for GotScience.org was published today. GotScience is a fabulous website with the goal of increasing the public awareness about science – a perfect fit for my goals and dreams! I adapted an article that I first published on this blog for GotScience about “What is a biobank?” (I think you can see a theme emerging). Please check it out along with the other articles on GotScience!

Finally, I’ve been helping out an editor friend of mine at PN Online – a magazine to help people who are wheelchair bound. I contributed to an article about this great new ALS research called “Early ALS Treatment.” I adapted my work for this article to a journal club blog post that you can read here.

I promise I’ll be back to writing on this blog soon, but until then, enjoy the articles I shared above!!

#WeCanICan #WorldCancerDay

A year ago tomorrow, I posted my first blog post. A year and nearly 100 posts later, I maintain the same mission I started with: to empower you with scientific knowledge so that you can make more informed decisions about your health.

February 4th is World Cancer Day, and they are running a social media campaign called “Talking Hands” so that people around the world can say how they take action to help prevent and fight cancer.  Besides what my biobanking team and the other clinical research teams are doing at St. Joseph’s Hospital and Barrow Neurological Institute to fight cancer, this blog is my personal contribution. I hope that in some way this helps you feel empowered to ask questions about yourself and your health, and in the case of a cancer diagnosis, feel better prepared to tackle your road ahead.

What can you do?

Photo Feb 02, 8 26 24 PM

How not to die when working in the lab – Biosafety

What’s your biggest concern for your safety when walking into work each morning? That you’ll get a papercut or burn your tongue on your morning coffee? Maybe if you’re in a higher risk profession (like a contractor) you’re worried about something falling on your head.  As a scientist, may researcher enter the lab every day and have to worry about being infected by what they are researching!

blood tubes

Blood tubes collected for our biobank

Human tissue and blood may contain viruses like HIV or hepatitis that’s just needs entry into your body through a cut or in the mucus membranes of your nose. Or maybe you’re working with viruses like the flu to see how they infect cells. And what of those people who are studying the deadliest diseases like Ebola – how do they study these diseases or work to develop vaccines or treatment drugs without getting Ebola themselves? BIOSAFETY!

Wow. Boring. Right? Well, kind of. I spent this last week taking a refresher course on biosafety and the reading was DULL, but sitting down to think about all of the implications it becomes fascinating.

The thing is, anything that would infect you is likely invisible.  If you’re working with human tissue or blood, you can see the blood but not what might be inside of it (bacteria or a virus) that could infect you.  And if you drop a blood tube on the floor, you can see the pool of blood but not the microscopic aerosolized droplets in the air just waiting to be inhaled. So how does a scientist take care of these hazards not just so they don’t get sick but so they don’t infect the public as well?

Good news is that scientists think about this a lot.  First, depending on what you’re working on depends on how careful you have to be. Compare this to the difference between giving a 4-year-old plastic play-doh scissors versus sharp surgical scissors – they have different risks associated with them and you’d treat the kid using them in different ways.  In the same way, working with things that are not known to infect humans and cause disease (like bacterial cells) don’t need to be handled as carefully as those that cause deadly diseases that are spread through the air (like Ebola).  This is what defines the “risk group” on a scale of 1-4, where 1 is the lowest risk and 4 is the highest. The play doh scissors or bacterial cells would be Risk Group 1 and the sharp surgical scissor or Ebola virus would be Risk Group 4.

This then helps researchers figure out what protective measures need to be taken – also called Biosafety Levels (abbreviated as BSL) 1-4.  For example, level 1 can be done in the laboratory out in the open wearing a lab coat and gloves.  Level 2 requires research to be done in a biosafety cabinet so that anything that spills or is aerosolized is contained.  Level 3 is for agents that cause moderate to severe disease and in this case the experiment needs to be completely contained in a glove box or in a special room with controlled air flow. Level 4 is for agents that cause lethal disease that has no treatment or cure (like Ebola). In this case the BSL-4 is what you may see on TV or movies where researchers are fully enclosed in a “space suit” to prevent any contact between the person and the agent.

biosafety

In my lab, we regularly work with human tissue and blood and because the tissue or blood may be infected with certain biological agents, they are considered risk group 2. We always wear a lab coat and gloves and work inside a hood.  When moving these tubes from one place to another, we make sure that there are at least two layers of containment – the blood tube is the first layer and this is inside a plastic bag as the second layer. We also get re-trained every year to make sure we remember how to handle spills (just in case).

Now because we’re all morbid creatures, I’m sure you’re wondering what’s happened when this hasn’t worked. Here is an article about the most common infections acquired in the lab and how they were acquired.  For more newsy stories, here is a story about a researcher who contracted plague in the lab. Eek! Definitely reinforces the importance of being careful in the lab.