How my PhD training has improved my baking skills

I walked away from the bench four years ago this month. Since that time, I have enjoyed the life of a Scientific Editor, where my training in the lab is integral to the job. I am still surprised when my training becomes useful in everyday life. Perhaps it shouldn't –  many articles about "The PhD Problem" focus on how training to be a scientist has other long-term benefits, including developing critical thinking and problem solving skills. A few years ago, I decided that I would start approaching recipe development like I would designing a protocol or experiment. This has been a very fun project, so I wanted to share my results.

First, I started reading more about recipe development by professional bakers. Then, I decided to tackle my favorite baked good: the oatmeal cookie. For many years, I have used my mom's recipe, which came from the Quaker Oats box and was never altered. They are delicious cookies, but as any scientist/baker would, I wondered if I could do better.


I had to figure out what recipe to start with. The Flour cookbook has a great oatmeal cookie recipe, with excellent instructions that are thoughtful about the science of baking (e.g., the formation of gluten). Another advantage is that their recipe includes weights for all the ingredients. The use of a scale to weigh ingredients was a crucial element for my recipe testing – it added precision and allowed me to make half a recipe (this meant I could bake cookies every other weekend without having too many extra calories). The Flour cookies are very good, but I found them too chewy and I wanted more oatmeal. I did some more research on how each ingredient in a cookie recipe contributes to the end result. (The best resource was The Food Lab.) Over the course of a year, I baked four different iterations of the Flour recipe and ended up with something in between their recipe and the original Quaker recipe. I have repeated this protocol six times and find it is consistently good – even after we moved (testing a new oven) and got new cookie sheets. Out of curiosity, I did try America's Test Kitchen recipe (free version here), as ATK is the gold standard of recipe testing. I found their cookie had a good oat flavor, but was too crunchy and crumbly. 

This experiment taught me a lot about recipe design and the small things that make a big difference in how cookies turn out (e.g., letting the dough rest overnight). I also found many useful resources to help me in future recipe development. It is definitely a great time to be a scientist/baker as there are so many food blogs and podcasts that focus on this topic. The success of my experiment and the wealth of resources available has encouraged me to approach my previously perfected "Test Kitchen Brownies". I will be sure to update you once my next experiment is complete.

DIY Science: Biopunk by Marcus Wohlsen shows how to do science away from the bench

I have read many stories about doing science away from the bench, both in the news and views section of scientific journals and on popular science blogs. PLOS Blogs even has a regular feature called Citizen Sci, which highlights how everyday people can take part in science outside the traditional laboratory or field setting. Thus, I was curious to read Biopunk: DIY Scientists Hack the Software of Life by Marcus Wohlsen.

Wohlsen did a great job of discussing what DIY science is and why it is important. Historically, the roots of DIY science can be found in people like Edward Jenner, who inoculated his gardener's son with cowpox to test its efficacy against smallpox and Newton, who poked himself in the eye to better understand optics. Today, the DIY science movement serves to democratize science, allowing people outside of research institutes and universities to take on projects based on their own interests rather than based on the decisions of funding bodies. As a result, the movement could transform science, taking some power away from the big companies that set steep prices for lab equipment.

One major goal of the DIY science movement is to MacGyer common lab equipment to make it accessible (read: cheap) to everyone. Some of these hacks could serve researchers that aren't lucky enough be in a well-funded lab. Take the example of the PCR machine, the biology lab workhorse that helps researchers copy and manipulate DNA (prices start at $3000). A Google search for "DIY PCR machines" reveals many designs that start at $100, making PCR available to more people. Thus, many of the projects in DIY biology can benefit the developing world because they are design to cut costs and to make it possible to run experiments in virtually any environment.

One element that seems to be common in every story about DIY biology is the comparison with the computer hacking movement. People turning spare rooms and garages into laboratories for their side projects does have similarities with the origin stories of companies like HP and Apple. The resemblance goes further: DNA is the code of life and, like computer hackers, people in the DIY bio movement believe that this code should be open source and not limited only to the scientists who have grant money or research labs. Labeling DIY scientists as "hackers" can create a negative impression; when the general public hears of a hacker doing genetic modification in their garage, there can be a tendency to overreact. The worst case was seen with Steve Kurtz, an artist that used the tools of DIY biology as part of his palette. In 2004, Kurtz was arrested on suspicion of bio-terrorism after his wife died of an unrelated heart attack. (There is also an interesting documentary about the case called Strange Culture.)

Wohlsen pushes the idea that DIY scientists are punks, describing their leather jackets, tattoos, and Mohawks, to the point that borders on fetishization of his interview subjects. To some extent, this is SOP in science writing (and celebrity interviews); it serves as a device to quickly characterize the subject. Unfortunately, it detracts from the serious science that is starting to happen. I look forward to seeing what DIY bio leads to in the future, especially because CRISPR technology has made genome editing simpler and cheaper than ever and it is readily available to DIY biologists.

Another great aspect of DIY science is that it can give the people who left the lab after their PhD or postdoc a way to return to the excitement of scientific discovery. Depending on where you live, you may find a hacker space near you. Here in Boston, you can visit the BossLab (Boston Open Source Science lab), but most major cities seem to have similar spaces available. Some more great resources can be found at DIYbio.org. Of course, I think I will keep my home experiments confined to baking. 

Resources for finding a career away from the bench

If you are a graduate student or postdoc in the sciences, you are likely aware of the "PhD problem"*, the academic bottleneck caused by an increasing number of PhDs with a concomitant decrease in the number of tenure track positions. Unfortunately, the statistics suggest that the problem is not likely to get better any time soon. In fact, the issue has gotten so bad that even the mainstream media has picked up the story. The default pathway is no longer PhD to postdoc to tenure track; this great infographic from ASCB  (see below) suggests that the tenure track is the real alternative career. While the statistics may seem grim, I think there is some good news: the academy is starting to wake up to the harsh reality**. In the past, postdocs and grad students complained that PIs were only capable of training them to become a PI. Increasingly, PIs and universities are aware of the prospects for their trainees and they are starting to find ways to help guide them for a number of careers.

ASCB.org infographic

As a Scientific Editor, I often get questions from graduate students, post docs, and PIs about my transition away from the bench. After a recent chat with a grad student at a meeting, I decided it was time to put together a post of useful resources for finding a career away from the bench. Because I am in publishing, my links tend to focus on that path, but all of the websites I list below have articles about other career paths as well. 

The first two places you should be looking for a job in science are Nature Jobs and Science Careers. Both websites have listings for a variety of careers paths as well as an array of great content for helping you navigate your job search. Whether you are just starting to think about your future directions or preparing for an interview and negotiating your salary, there are relevant articles for you.

Nature Jobs has a very well-organized site. I recommend spending some time there to explore their content, especially their blog and their career toolkit. This article from their blog gives a great general overview of the types of jobs available to people with a PhD in the sciences. Be sure to check out The Postdoc Series for articles aimed at post docs at different stages of their careers. Nature Jobs also hosts a career expo, which I have read good things about.

On the Science Careers website, check out the tips and tools and explore the articles in the Career Magazine; they have more than 10 years of content available. By far the most valuable resources I found when I was searching for my current job were this collection of articles about science writing and editing and this 2002 article "Careers in Science Editing". These give a very general idea of what different types of scientific editing jobs entail. This informative article from Cell Press' Debbie Sweet describes the specifics of working for a reviews journal or a primary journal. Once you find something of interest, the related article feature (which seems to be available for newer articles only) will help you find more to read.

Societies relevant to your field will likely also have career resources available. For cell biology, ASCB's Career Development section has a number of articles available. My favorite among these is the Career Publications, which are free to download as PDFs. The ASBMB also has some useful articles, like these Career Case Studies.

The Chronicle of Higher Education is generally best for searching for a faculty job, but they also have some excellent articles on non-academic jobs, such as "The PhD's Guide to a Non-faculty Job Search".

If you are feeling isolated in your decision to leave the bench, you can find some comfort by reading some "quit lit". It seems many scientists find it cathartic to share their story;  indeed, I have written my own quit lit posts on this blog (here and here). Over the years, I have read many posts in this genre; I particularly enjoy finding updates, which tend to have a happier mood than the original post. Eva Amsen's (Outreach Director for Faculty of 1000) "Five Years Later" was very positive and shared some useful links and tips. Likewise, SciCurious (a science writer in neuroscience) tells her story in "The system failed me. It should have failed me sooner." 

To learn more about a career in science writing, read Ed Yong's collection called "On the Origin of Science Writers" where a variety of working science writers share their journey as well as tips on how to make a living writing about science. The National Association of Science Writers also has some great content in their resources section.

In short, these links should give you some ideas of the paths that are available to you. Hopefully you also have some valuable resources at your institution (e.g, postdoc association or a career development office). If you find other useful links, please share them in the comments. 

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* There are numerous suitable links that describe the problem; I have chosen the one that I first discovered. Nature had a 2011 special issue called The Future of the PhD, which included the great story The PhD factory.  

** The Future of Research symposium has been putting together meetings to find solutions to these problems.

Oh, the places I go! Another reason I love being a Scientific Editor

My job as a Scientific Editor gives me the opportunity to read much more broadly than I did when I worked in the lab. While researching manuscripts for suitability for the journal or while trying to find reviewers, I sometimes end up in very unexpected places. I discussed this briefly in my post about the book Elephants on Acid and Other Bizarre Experiments. I often find myself reading abstracts for papers that sound like fodder for Seriously, Science (formerly known as NCBI ROFL). The premise of this site is simple: post abstracts from PubMed with a simple description of the work. Of course, they tend to choose papers that sound pretty ridiculous on the surface. These are typically the types of papers that would garner criticisms about why such research should be funded. Here are some recent examples: "Study proves 'old person smell' is real"; "Curvy vs. straight - which glass ups your drinking rate?"


As a graduate student I studied the motility of the sperm from Ascaris, an intestinal parasite from pigs; we affectionately called our system "worm sperm". Thus, I understand the appeals and perils of working with an offbeat system. These unusual systems actually have important applications (otherwise they would not likely be funded). For example, worm sperm has a novel machinery for cell motility (more specifically, it uses a completely unique protein to power the movement of its amoeboid sperm), which could help us understand how more traditional cells crawl. Studying simple cells to understand more complex ones is a common approach in cell biology. The idea is that there should be conserved elements that should be comparable between the different cell types; such an approach can allow scientists to generate a minimal parts lists for a cellular process of interest. Thus, brewer's yeast can be used as a model system for a surprising number of cellular processes, even neurodegenerative diseases like Huntington's and Parkinson's.

A few weeks ago, I was looking for reviewers for a paper about protein stability during cryopreservation of heart tissues (now available in BBA - Proteins and Proteomics). The work could eventually have an impact on how tissues are stored prior to tissue transplants.  I found myself reading title after title about the stability of proteins after cryopreservation of semen of various types, especially boar and horse semen. The funny thing was -  I was not surprised to stumble upon these papers because I had seen them before. On the previous occasion, I was researching a paper on the proteomics of horse semen. These areas of research might elicit some giggles even from the seasoned scientist, but the work could have important implications for animal husbandry.

I recently evaluated a paper that described the protein in Venus fly traps responsible for digesting arthropods. Interestingly, it is a chitinase, an enzyme that can break down the chitinous exoskeleton of the fly trap's lunch (now published in BBA- Proteins and Proteomics). While searching for reviewers, I found a plethora of interesting papers, such as the mechanics of the opening and closing of Venus fly traps and proteomics to identify the components involved in digestion in a variety of carnivorous plants. I also see a lot of papers about insect venom. For example, we recently received a paper about the proteomics of fishing spider venom. As I learned in the book Wicked Bugs, insects and spiders have some pretty amazing (and terrifying) ways of attacking their prey. Some recently published papers demonstrate that understanding how the venom works can be useful for developing new pain killers as well as novel pesticides.

Every week I seem to find a new and strange corner of PubMed to explore. Sure, I still have some knee-jerk reactions and giggle when I read some of the titles. Generally, though, once I dig deeper to understand what the long-term goal of the work is, I tend to be amazed at the boundlessness of scientific curiosity and the ingenuity of scientists for finding new ways of solving problems.

My year away from the bench

It has now been one year since I left the lab. In May 2012, I found a full time position as a Scientific Editor for BBA with Elsevier in Cambridge. It is an excellent job for me: I get to read other people's science all day. Plus, it has been an exciting change of pace. In the first few months, it was tough to get used to the relaxed atmosphere; suddenly, there was much less pressure to produce results. I have since adapted to the vagaries of scientific publishing. The best part of this normal schedule: I have a more balanced life again. For me, this has included reading more books, watching movies, and running more regularly. 

I have also started to develop my skills as a baker. Anyone who has tried my brownies knows that I am familiar with the power of combining eggs, butter, and flour. However, in the past few months I have started to take this to a new level. About six year ago, I stumbled upon Cook's Illustrated/America's Test Kitchen. If you are unfamiliar, they have an amazingly scientific approach to developing a recipe; essentially, they make 100 batches of chocolate chip cookies so you don't have to (by the way, their chocolate chip cookies are amazing and are worth every extra step). I started to think about my baking differently. I have been reading more about the science of cooking, specifically the chemistry of the ingredients and how changes in the ratios of the components can lead to predictable changes in the resulting product. 

I decided to work on one of my standard recipes: the oatmeal raisin cookie. In the past, I have done a little bit of experimenting with my recipes, but I have never been very methodical. For this new undertaking, I invested in two new tools: a scale and a notebook. After a few batches, I think I have a successful recipe, which has consistently (N = 3)  achieved the desired outcome: a cookie with a good combination of chewy and crunchy with a lot of molasses and oatmeal flavor. 

I suppose this means that I miss the lab more than I had anticipated. Of course, in contrast to experiments in the lab, a bad result in baking is still a good outcome: treats to enjoy! 

   

   

I am the 80%.

My decision to leave the bench has not been an easy one.  

I have been applying for jobs, and I found myself writing this sentence for my cover letter.  This seems like such a simple sentence.  It feels rather cliché.  It is definitely an understatement.  In reality, the past year has been wrought with tears and anxiety. 

The reason the sentence feels cliché is that it likely is.  The academic bottleneck is a reality that many post docs in science will have to face.  The likelihood of a post doc in the biological sciences landing a job as a PI is pretty low.  In the seventies, 55% of PhD's would have a tenure-track job; in the past decade the number is closer to 20%.   (More cogent articles have addressed this issue, e.g., The PhD problem and The PhD Factory, so I will not belabor the point here.)  Nonetheless, lots and lots of post docs brave the odds and join a lab. What drives PhD's to keep making the leap of faith?  Judging by the behavior of my lab mates, who tirelessly toil away for 60-70 hours a week, it is somewhere between passion and madness.  I recently heard one lab mate, upon being asked what she would do if she weren’t a scientist, reply simply and without a trace of drama, “I would die.”  Is it this simple?  Like an artist or a writer, some people are just called to do this and could not consider an alternative. 

Goodbye bench.

In my case, I feel I was lucky to stumble upon this job in the first place.  As my project comes to a close, I find myself questioning why I ever spent all that time in the lab.  Of course, I was like the others: driven by the pursuit of the answer to my question, in search of the perfect experiment to make the paper that much better.  No matter how sad I get about the fizzle of my project, I try to recall the days when I knew that I could beat the odds and get my own lab and do some really great science.  I am still jealous of those that are living the dream, and I hope that they can make it work.  

For me, I am embarking on a new stage as a science editor and writer. I will be sure to keep this blog updated as I progress.