Life in fluctuating environments

By Jen Nguyen

Lately I’ve been caught up with bacterial growth. Like the kind that spreads over raw cheese, forming a rind and eventually flavor. While the development of this colony is in itself fascinating (and delicious!), it’s not what particularly gets me – I’m amazed that growth even starts.

During my last visit home to California, I toured Cowgirl Creamery and sampled Red Hawk: a lovely cheese with a lovely story. The rose-orange color, corresponding bacterium and taste were all a product of an accident. A protocol gone wrong. (Or right, depending on your perspective.)

As the story goes, a batch of aging cheeses was neglected and the culture overgrown. In a half-ditch effort to save the batch, the rounds were scrubbed in salt water and left out to sit. An unusual blush developed, someone dared to taste it, and – as chance would have it – a novel market item was born.

Red Hawk’s unique appearance, odor, and funk derive from a marine bug of the genus Brevibacterium. Apparently these bacteria float around in the Point Reyes air, drifting until they encounter a round of adolescent cheese.

This is incredible to me. Not the part about marine bacteria in air; waves break, droplets dry, and particles aerosolize. But that a bug isolated from seawater and fish guts can then travel via air to grow in a substantially different habitat, is that not remarkable? This bug didn’t book a plane ticket to Cowgirl. Rather, it was repeatedly thrust into new environments and succeeded greatly.

Now I risk anthropomorphizing, which is a dangerous thing, especially with microbes. Our intuition about the world largely fails if we try to impose it onto theirs. But be as it will, my awe stems at least in part from my attempts to empathize. Sure, life happens. But I don’t imagine I’d do all that well if I was unexpectedly cut off from food for even a handful of hours.

By comparison, our lives seemed too good to be true. A reliable food supply, the promise of shelter – what luxury! Especially as a middle-class resident in the Golden State, which boasts only a miniscule fraction of the country’s farmland yet produces a hefty claim of the crop. With naïve nostalgia I would refer to California as “the land of wonder,where everything grows. That was until I realized that I – like bacteria depend on resources that are not under my control but the environment’s.

Last month, my family sent me a box of persimmons grown from a tree in our backyard. (For those who have never tried a persimmon, I highly recommend.) Happy nevertheless to have had them, I couldn’t help but notice their meager size, odd texture, and poor taste, presumably an effect of California’s now three-year drought.

Because the West depends on accumulated snowmelt for a majority of its water, the climate largely affects key commodities, such as sanitation and agriculture. As our reservoirs diminish, the availability of water changes. And when the available water becomes sufficiently mismanaged, we’ll find ourselves cast in a real-life production of Urinetown (a musical, also recommended), whether we like it or not.

While we can’t force snow to fall, we can control how we respond to environmental limitations. During the Big Dry, a drought that lasted about a decade, the Australian government spent billions on support packages for farmers. In California, farmers are investing into new groundwater wells. Will these actions succeed over the timescales we require?

This brings me back to bacteria and my ever-deepening respect for them. Their solutions may not be ours. (It may not matter to them if a skewed resource distribution forces the majority to die. And they are likely less fickle and demanding than we.) But this uncanny ability to live – and perhaps thrive – in wild fluctuating environments is an admirable trait.

Perhaps limiting ourselves to one song in the shower, or pay-per-use toilets, or choosing desert stargazing over desert golf, seems somewhat restrictive. But life on Earth has existed for billions of years in exceedingly restrictive environments, probably even more so than that of marine bacteria today (no cheese). The world fluctuates. Life learns to live within nature’s limits, and I realize I am no exception.

Image credit: Benjamin Wolfe

Two PhD students walk into a bar…

By John Casey

While quietly reading in my favorite watering hole recently, I was accosted by a well-lubricated and gregarious compatriot. Steve scooted over several bar stools and introduced himself as a PhD candidate at Harvard. He proceeded to interrogate me with shotgun queries about my own graduate work – e.g., “so what’s the difference between a virus and a protein?” and, eventually, “how many RNAs do you need to make a peptide?” After significant explanatory efforts, punctuated with rough sketches of molecular structures, I grew impatient and asked him what, specifically, he studied. I was met with a dramatic pause. “… Time.” Further exchange made it clear that Steve was not studying time as one thread in the four-dimensional fabric of physical reality. Rather, he sought to challenge our culture’s (apparently) rapacious, exploitative tendencies to measure it in the first place.

Of course, most of us need not know precisely what an amino acid looks like. And perhaps one can articulate useful ideas about the perception of time while entirely oblivious to physics. The conversation nonetheless reminded me of a frustratingly stubborn, population-wide level of scientific illiteracy. Technological advances are the only real solution to maintaining or improving quality of life in the long term, and it is critical that the citizenry develops a basic fluency in scientific issues.

There are two arms to my argument that public scientific literacy is more important than ever, and growing more important by the day:

1) Worldwide population growth heavily strains our standards of living, impeding our abilities to feed and empower ourselves, with attendant risks both acute (Ebola) and chronic (water shortages); and

2) The nations with the greatest power to confront these strains, aside from China (for now, CPC…), are democracies which rely upon citizens to select policy makers.

Science, alongside a period of relative peace, has allowed humanity to cross 7 billion souls. We know how successful fields like agriculture and disease theory have been – happy 100th birthday, Dr. Salk. In this sense we as scientists can congratulate ourselves for perpetually snowballing our own importance. Fewer infections translates to more cancer research; greater crop yields will indirectly boost energy demands. On and on, science pushes back a hypothetical Malthusian equilibrium. In managing safe food options, the budgetary effects of the drug development industry, or the long term implications of various energy options, science has by necessity migrated to the core of national and international policy. Yet those ultimately responsible for 21st century science policy – the electorate of the world’s democracies – remain vulnerable to cynical politics due to a sore lack of science education. And no, scientific incompetence isn’t partisan: for every climate change skeptic on the right, an anti-nuclear energy advocate on the left charges his electric car with coal-based electricity. Neither is the problem domestic. Europe seems as unreasonably obstinate about “genetically modified organisms” as the US is about its energy sources. China has, perhaps similarly, determined that GMOs are an American conspiracy to poison their population. Fear of modern science allows polio to linger at civilization’s edge in places like Pakistan (sorry, Dr. Salk). Skepticism toward modern medicine seems also to have exacerbated the spread of Ebola in regions of West Africa; the coming decades-long boom in Africa’s Sub-Saharan population is likely to accelerate future disease outbreaks if that populace remains poorly educated.

Even the gravest security issues of the day are interwoven with science and technology. The highest hurdle to Ukraine’s autonomy, in the face of Putin’s quiet insurgency, is its reliance on Russian fossil fuels for energy, a situation shared by most of Europe. The ongoing conflicts in places like Libya and Syria are thought to have been potentiated by frustrations with local food and water shortages, and Iran’s own putative energy needs complicate any clean resolution of the region’s chaos. Scientists employed at the US State Department are playing larger roles as international relationships struggle in the face of, for instance, violent cross-border conflicts over deforestation.

Here I argue that we, on any long term scale of society, can maintain neither peace nor our standards of living without more scientifically literate decision-making; it is equally essential that we, as scientists, engineers, and medical professionals minimize our own biases. Allowing any contaminant ideology or self-interest in proffering our science will only lead to greater distrust on behalf of those we need most: the voting and taxpaying public. While efforts within US science agencies to improve communication between its scientists and the broader public are gaining momentum, immense gaps seem entrenched for the foreseeable future.

All of which brings me back to Steve. It’s disappointing enough that a student as successful as a PhD candidate, humanities or not, at the world’s premier university has not been asked to learn the most basic concepts of life science. After all, if a highly educated millennial student can’t remember the difference between nucleic acids and viruses, why shouldn’t most people be terrified of GMOs and viral outbreaks? What’s also disappointing, though, is my own clumsiness and impatience attempting to fill in his porous grasp of biology. It will require a stronger, broader effort from many of us, not only to enhance scientific development during K-12 education. Hopes for prosperity will also require that we help the public understand, at a functional, sociopolitical level, the implications of contemporary science & technology.

Making friends; scooping enemies

By Scott Olesen

I read a perspective piece on an article written by a grad student G in another country. G said he wanted to pioneer a therapy T to solve a problem P. I want to pioneer the same therapy T to solve the more important problem Q. Along the way I would also solve G’s problem but in a smarter and better way.

When I read the perspective piece, I felt envy, jealousy, excitement, and shame. Envy because he got a paper and a perspective piece. Jealousy because I like to think therapy T is my idea. Excitement because I want to team up with G to solve problems P and Q. And shame because I want two things: to be his colleague and to scoop him. Shame because even here, on this blog, I use the ridiculous designations G, T, P, and Q—so I won’t get scooped.

I like science in part because it does good for people. Solving problems P and Q will make many peoples’ lives a little better. I like the idea of the academic community getting together to solve the world’s problems. If G and I team up, we can have a great time talking about T, P, and Q over the beers of our respective nations. We might solve P and Q faster and better than if we work alone. But I want to graduate, and maybe I want an academic position, so I need papers, and for papers I need to pump out a good project before someone else does. I need to scoop G.

I came to science dreaming of a glorious commune—maybe like what hippies want to make out of acoustic guitars and old buses—where scientists think hard and work hard and make the world better. Instead I find Adam Smith and the invisible hand, the NIH funding two researchers who work on the same problem, each pushing science ahead by trying to scoop the other. When a PI does this, we call it a toxic lab environment. When the NIH does this, we call it a thriving research community. It seems that G must be scooped, and I must scoop him, for the good of us all—but mostly me.

Finding a job out of grad school (n=1)

By Felix Moser

I graduated a year ago and spent much of that year looking for a job in industry. The decision to find an industry job was a mindful one. Like many graduate students, I was unsure what I wanted my long term career to look like. The ideal scenario of becoming a professor seemed fleeting, given the funding climate and level of competition for academic jobs. Climbing Everest seemed less challenging. So, I decided to pursue an exciting R&D job at an innovative company. I was motivated by a desire to immerse myself in a different environment and understand the needs and process of industrial science. I wanted to learn how to create value and how to focus research on generating that value. Though I loved academia, its freedom and flexibility, I felt I might grow more as a researcher in an industrial lab. So, I set out to find an industry job. I assumed that with an MIT PhD in a hot field, I would have options.

That turned out to be a bit presumptuous. After sending my CV and cover letter to dozens of companies, a half dozen phone interviews (several with friends who had their own start-ups), and three in-person interviews at Boston area companies, I had no offers. I was very frustrated. What was I doing wrong? I had gone to many career workshops while at MIT, including several very useful ones by the BE writing lab. I had spent serious time editing my CV and cover letters, tailoring them to each company I was applying. Writing fellows read them and gave me valuable feedback. I practiced interviewing, I practiced my job talks. I printed business cards and went to networking events. I even got a friend to take good headshots for my linkedIn profile. I thought I had done everything right. So, what was missing?

I came to a few conclusions. I should say that one of these is that the job search is very individualistic and that there are no hard rules for success. I should also say that I was picky. I wanted to do research that excited me, and I would not compromise on that. This narrowed down the possibilities considerably. Maybe this was unreasonable, but at this stage in my career, I felt I could and should allow myself that luxury.

Most prominently, perhaps obviously, I realized that my skill set was not sufficiently marketable. I’m a genetic engineer. This involves two skills: designing the genetics, and building the DNA. The building portion (a.k.a. cloning) can be done more cheaply by technicians or (at higher scale) with robots. The designing portion requires considerable knowledge and experience with an organism and molecular systems. Unfortunately, not many people value E. coli genetic engineering sufficiently to need many PhD’s doing it. So, basically, I was too expensive to hire for the manual labor alone, and genetic design was not in high demand. Searching through job postings by biotechs, I did notice skill sets that WERE in higher demand. These included big data analytics, bioinformatics, software engineering, mammalian tissue culturing, process engineering, and anything pharmaceutical development. I found myself wishing I had done more programming and knew something about CHO cells.

I also realized that most job postings were looking for people with 3-5 years of “experience.” By the time I graduated, I had worked in biology labs for over a decade. I thought that counted as experience. Turns out that any time spent in school is considered baseline. The only “experience” that stood out on my CV was a 3 month internship at DSM, a big Dutch chemical company. I think this is because it was time actually spent in industry. Companies are very wary of academics transitioning to business for the first time. Many have trouble working in business, which requires more teamwork, clear communication, and flexibility. My internship alleviated some concerns, but it wasn’t enough. I began to realize what 3-5 years “experience” meant: a postdoc. I was competing, fresh out of grad school, with people with identical education but more experience. And there’s a lot of them out there. I concluded that doing a postdoc, once an optional training period before becoming faculty, has become a prerequisite for many entry level scientist positions in industry.

Lastly, I realized that many of the companies I had applied to had recently finished rounds of hiring. People I knew with my exact qualifications got jobs at companies I applied to, but they applied much sooner than I had. Because timing is not something we have a lot of control over, many people leave it out as a point of advice. But timing is important. If you graduate right when a company closes its series B funding, then the odds of you landing a job are much higher, because they need someone NOW. If you apply a month later, you might not even get a reply. My advice is to build relationships with companies and their employees and keep in touch with them. Inquiring regularly might position you at the top of their list next time they start looking for to hire people.

In the end, I became frustrated with the repeated rejections and the relative dearth of new opportunities, so I stopped looking. I decided to stay in my graduate lab as a postdoc. My project had reached a point where I could write another paper, and my advisor was supportive. I love working at MIT and feel at home in Cambridge, so I was in no rush to leave. Perhaps staying in the same lab was a mistake, but I felt it de-risked several issues, such as funding and working with a new advisor. Advisors like postdocs who stay on 3-4 years to finish projects and go to academia, and I was doing neither. To gain some new skills and knowledge, I picked up a project doing metabolic engineering in yeast and have been proactive to improve my coding skills. Once I finish my current project, I will wade into the industrial job market again, this time with a few years extra experience and some lessons learned.