E. coli Up Close and Personal: Scientific Rockstar and Public Enigma

It seems nothing puts fear in the hearts of the masses like mentioning E. coli. Most think of the disease-causing germ that contaminates everything from spinach to beef. I agree the strain Escherichia coli O157:H7 and its cousins O26, O145, STEC O104:H4, and others, are a wretched bunch that give the whole species a bad reputation. What makes these strains so vile are the extra proteins encoded within their genome. For example, E. coli O157:H7 has a larger genome coding for 5561 proteins while the parent strain E. coli W codes for 4739 proteins. Thus is the life of a bacterium. The fact there are so many bacteria means they are usually in close proximity to each other. Physical contact between bacteria, not just those of the same species, allows for the transfer of genetic material between two cells (horizontal gene transfer); the closest thing to sexual reproduction you will find for prokaryotes. If the genes transferred to the recipient give it an advantage or new ability that helps it compete and thrive in its environment, they will remain in the genome. Otherwise, they will be discarded after genome compaction.

Most E. coli are completely harmless and, in fact, beneficial. If the general public knew more than what was broadcasted on the 24 hour news channels, they would see the tiny rockstar scientists have known about for some time now. Beginning in earnest in the 1950s, E. coli is easily cultured in laboratories and very cheaply. Its quick generation time (20 min. at optimum temperature) made it a great model organism to study in many fields of science and medicine. This organism is the work horse of biotechnology due to the relative ease of manipulating its genome or adding complete genetic circuits into the cell using plasmids.

Sidebar

Even after 50 years of intense research, E. coli still holds many unknowns out of the reach of our knowledge. Like all other sequenced genomes, there are a number of “hypothetical proteins” and “proteins of unknown function”. This means by our best abilities, we can locate parts of the genome that code for proteins, however, this doesn’t mean we are able to understand the function of a particular protein.

Image courtesy of Predrag Radivojac. Thanks, Pedra.

The above shows just how much work is left to understand the biological capabilities of Mother Nature. Short version: over 40 gene sequences in databases, but the number of which that we know what the function is holding steady around 500,000 and the number of solved protein structures is over 100,000. This is a growing gap between the known and unknown.

 Where would we be without E. coli?

One advantage of E. coli is their effect on our immune system. Some may find this counter-intuitive, but E. coli can lower the workload of our immune system when pathogens are present, especially in the intestine. When E. coli attach to the GI wall, it changes the acidity of the lining thus making infection from other bacteria less likely. Another benefit is in overall digestion. E. coli promotes better breakdown of food thus preventing accumulation of waste which is a major cause of bloating and constipation.

Many outside the scientific community may not be aware of how integral E. coli are to the advancement of many fields including medicine, pharmacology, biology, and even human physiology. Another reason to not believe the hype.

Wanted: A Nation of Bill Nyes. Making science mainstream, fun, and relevant again

The United States rose to superpower status through a necessary, aggressive push towards innovation and scientific discovery in the last century. Many of the technologies developed in the last one hundred years were products of research funding by the U.S. government. In the old days, the gap between discovery/invention (public sector) and product development (private sector) was more easily traversed and companies were more than willing to take that leap. What scientists and engineers viewed was almost certainly drastically different from what consumers viewed, but either way, it was progress.

The world is a much different place now. Research funding (minus stimulus funding) has remained stagnant and the outlook is bleak.

One of the overlooked aspects of this funding is the community outreach and broader impacts that result from grants. This includes money for paying undergraduates and graduate students for research conducted in the grantee’s lab. From personal experience, most of the undergraduates that came through our lab when I was a graduate student were STEM majors. However, this is misleading because the goal after receiving their B.S. was to attend a professional school including medical, dental, and pharmacy schools. To date, only one out of twenty or so undergraduates from our lab later attended a STEM graduate program.

Why aren’t more students interested in STEM?

“A society’s competitive advantage will come not from how well its schools teach the multiplication and periodic table, but from how well they stimulate imagination and creativity”

-Albert Einstein, 1953

“Bear in mind that the wonderful things you learn in your schools are the work of many generations, produced by enthusiastic effort and infinite labor in every country of the world. All this is put into your hands as your inheritance in order that you may receive it, honor it, add to it, and one day faithfully hand it to your children.”

-Albert Einstein, 1934

Many professions have had their icons and role models. Einstein is arguably the most famous scientist to walk this planet. When once asked what was the best advice he could give to people, he said to always remember to put the shower curtain inside the tub before turning on the water. He had a sense of humor that made him relatable to the masses even though he saw the wonders of Nature as math equations. Einstein wrote a lot about curiosity, imagination, and enthusiasm. These qualities can be used in many ventures, but he chose Physics.

Segway…

Bill Nye has never been accused of lacking enthusiasm. Having a genuine curiosity of how things work led to a degree in mechanical engineering. Most of us, however, know him as the Science Guy on TV. Spanning 100 episodes, Bill Nye the Science Guy laid a foundation for many across the country to explore curiosity and imagination. Nye took on current, relevant topics and made them relatable and understandable for children (and their parents).

For me, these shows were a time for exploration (virtually). I was able to better comprehend myself, nature, space, chemistry, etc. Times have changed and most people receive information from a variety of sources, some much more interactive. The technology to inspire children to pursue STEM careers are out there. However, where are the enthusiastic STEM crusaders and icons? Unfortunately, it’s not the teachers. They are too busy teaching mandated facts in a race to get through all the course material before the standardized tests in the spring…

As many have noted, the number of students who pursue a career in a STEM field fall well short of the demand from industry and see this as the problem. On the other hand, I see this as the result of the problem. At some point between toddler years and middle school, the inherent curiosity of a child fizzles; overtaken by media and gadgets. Have a question? Look it up on the Google app (I’m not criticizing Google. It is the best tool for any scientist). We, and our children, are constantly connected to everything going on in the world. For some it is politics or business, but for our children, it is Justin Bieber and Taylor Swift. To me, again, this is not the problem.

Let’s take a couple of other celebrities as examples: Brad Pitt and Will.i.am. We all know Pitt as an actor, however, we know him just as well for his charity work through the Jolie-Pitt Foundation. Will.i.am is a musician but is also into science as seen through his support for FIRST (For Inspiration and Recognition of Science and Technology) and its robotics competition. These are two examples of celebrities using their fame for a greater good.

STEM has an image problem in the United States. (A great survey sponsored by Microsoft showing the perception of STEM by students and parents can be found here). According to a study by Lenovo, the second leading hesitation to a career in STEM for U.S. students is that it requires too much work or school. The number one reason being that the student doesn’t feel confident in their ability. Here is the disconnect…if the passion and curiosity of the world around you and how to make it better is not there or hasn’t been curated, a STEM career is considered too much work. My Ph.D. took 6 and a half years to complete. I never once considered giving up or considered it too hard or too much work. To me, it wasn’t work. I felt lucky to be able to do what I loved and get paid for it.

In my humble opinion, keeping a child’s curiosity and imagination alive is a major step towards having real progress in attitudes and participation in STEM education. I personally wanted to be a doctor growing up. I was fascinated with how all cell types worked together. The checks and balances. As I grew older, in came the question of what specialty to go into as a medical professional. Knowing my interests, it seemed no ‘specialty’ was specialized enough. Then while working at a summer internship at the Oak Ridge National Laboratory, I went into an office with the Biochemical Pathways wall poster.

I could not take my eyes off of this masterpiece. To me, this poster symbolized life at the smallest scale but yet so sophisticated and precise; not to mention the signal transduction pathways that mediate the pathways output at any given time. I had found my calling. This visualization of what I had been taught in biology classes at all levels and biochem classes in college came to fruition.

For others, I’m sure it is different and I’m sure it’s not for everyone. The goal, inspire as many as possible to explore their curiosity of how life works and how they could make it better. Now the question, how do we do it?

The Microbiome: Can We Please Consider the Human Body an Ecosystem Now?

It has long been thought the type and amount of microbes using the human body as a home shape the way we live and behave. The microbiome as it is known is shown to have a greater and greater impact in our daily lives.

A new study published in Nature (paywall) provides evidence demonstrating the artificial sweeteners we all love and consume to control weight leads to increased blood glucose levels. How can something used to replace sugar in consumables raise the amount of sugar in the blood?

Like many other answers regarding human health, look no further than the microbiome. Consuming artificial sweeteners alters the composition of the intestinal microbes leading to a growing glucose intolerance. The researchers linked artificial sweetener use to altering metabolic pathways within the microbiome that leads to increased susceptibility to metabolic disease.

To verify their findings, researchers gave antibiotics to the mice used as models thus reversing the effects of artificial sweeteners. Results were also verified by using fecal transplantation in the mice to reverse glucose intolerance.

The Human Microbiome: Our Ecosystem

We already knew the microbes outnumbered our human cells 10 to 1 and that the microgenome outnumbered our human genome 100 to 1. The evidence is growing suggesting our normal flora govern more of our lives than we naively assumed for decades. We are not individuals but individual incubators for the microbial overlords that we could not live without. Just like other ecosystems, changing our lifestyles have a complicated effect on system as a whole. Small alterations to the microbiome can have major impacts and be the difference between health and disease.

Future posts will hopefully provide evidence demonstrating how we are shaped into individual ecosystems. Thank you, microbiome.

 

A Career Change is Quite Literally a Dream Changer

Career change and dream change

Those who may know me also know I can have weird or vivid dreams on a regular basis. For as long as I can remember, I have had dreams of tornadoes at least once a week. Another recurring dream subject for many years has been airplanes. Me on an airplane. You might not think anything of it, but some of these ‘airplanes’ were actually non-flying objects like a passenger van or a pharmacy in the basement of a local hospital I used to work. One of these dreams I clearly remember because I was flying the plane from a second cockpit in the plane’s ‘attic’ and had to continuously put oil on a gear to keep the plane in the air.

Over the past year, these airplane dreams have expanded to airports. Me in an airport. You might not think anything of it, but some of these airports were very small; the size of a restaurant (with bar). A year ago, I lost what I considered the perfect job promoting and writing about science emerging from one of the Departments of the U.S. The airport dreams started around the same time I was laid off.

I recently had a dramatic change in my recurring dreams. I no longer am at an airport or on a plane between airports. Suddenly, my method of transportation was not by air, but by sea; ships, cruise ships to be exact. Sometimes these ships were floating hotels with thousands of people watching high school basketball or attending a conference. Sometimes my family was on board and other times I knew no one aboard the boat.

I recently had a career change from science writer to science instructor at a local college teaching the wonderful subject of Biology. This is something I am very fond of and no stranger to with my Ph.D. in biochemistry, cellular and molecular biology. My passion for promoting science to the masses had to be honed to promoting science to the classes.

What does this have to do with dreams?

Dream interpreting is not one of my hobbies, but this one is quite easy for me to discern. Airplanes are a way to travel great distances in a short amount of time. One can cross the globe and be back home in a day or so. Imagine the sheer amount of contact a person can have with people on that journey. The airports were just a mode of transition. The dreams were no longer about flying but instead about what happened after landing. It was time to slow down.

What about the cruise ships? Ships don’t travel at break-neck speed, but they can get a person across the ocean or gulf and back within a week or so.This leaves ample time to explore the ship and get to know the people aboard; learn their stories and backgrounds. It gives time to tailor your message to those whom you see daily for a period of time until the next cruise when you start over with a new group of passengers.

 

There you go; a career change from science writer to science instructor. Or, as my brain sees it, jet setter to cruise ship director perhaps.

 

Now, if I only knew what the heck all the tornado dreams were about…

Graduate School Does Not Prepare Students to Teach Effectively

3D bacterial cell illustration, bacteria,

Graduate School is Great

Don’t get me wrong. I enjoyed most of my experience while in graduate school working towards my Ph.D. I was paid to fuel my personal curiosities about how bacteria make choices. It was a win-win in my opinion. I was contributing to the overall knowledge of the scientific community and making connections that I never would have dreamed of years before. I could safely say no one on the planet was investigating the same phenomena I was, so I held knowledge only I knew. Pretty amazing feeling. I read some article in Science Careers long ago about advice for graduate students. One nugget was that the student needed to become the expert of their project, not their advisor. I tried to make that my goal and knew I was succeeding when my advisor would ask my advice about observations she was making in the lab.

Graduate School is Good

Don’t get me wrong. Graduate school was not all a field of lilies. It was hard, very hard. Blazing trails and keeping up with all the latest research from around the world about my topic was daunting. Then, there was the preliminary exam (aka qualifying exam); six weeks of taking on an entirely different topic, becoming an expert, devising experiments to answer research questions, writing a full grant proposal, presenting to the department, and defending your ideas for hours is not for the faint of heart. However, the prelim (I had to go through twice) is like being thrown into the ocean as an infant and told to swim the English Channel. If you make it, you are a much better scientist for it. It was HARD, but I don’t regret all the effort it took.

Graduate School is O.K.

Working in the lab can be very time consuming. Many lab bosses expect the grad students to be in the lab 60 to 80 hours a week. I should have been in the lab more, I admit, but I also had a wife and a daughter the last couple years. I had a lot of expectations of me not only as a student and a training scientist but also as a husband and father. Only one of these four expectations was I an expert at after 25 years of schooling. Being spread so thin made each facet that much harder. Needless to say, my wife (and daughter, and in-laws, and parents, and brother, and the rest of the family, and friends, etc.) were very excited when I finally saw the fruits of my indentured labor.

Graduate School is Absolutely Horrible

Don’t get me wrong. I had opportunities to ‘teach’ students during graduate school. I taught a few semesters of lower-level biology lab sections early on. I enjoyed trying to make connections for the students. I remembered when it all came together for me and the light clicked. I wanted that so badly for my students; and much earlier in their academic career.

Now I am out of school with a degree I am very proud of. At what point in graduate school was I supposed to become an expert teacher? Much emphasis is towards shaping an independent scientist who can survive in the jungle, and rightly so. But, what about an emphasis on one of the tenets that come with many job descriptions those fledgling scientists would eventually end up with: instructing? No courses, no seminars. Am I missing something? Is the arena of instructing young minds preparing them for the future jobs we need them to take and excel at not important?

I am very fortunate. I have a faculty position now. I am an expert…but not at what I am expected to do, teach. I am a novice, an infant trying to very quickly consume as much information in teaching strategies and instructing styles that I feel I should have been exposed to in school. Do the science departments and education departments of our colleges and universities know of each other’s existence and absolute need for integration?

I want to be the best instructor ever. I want my students to get it every lecture/class meeting. I want them to appreciate the world around them and make logical decisions. Is that too much to ask? It is for the current state of a majority of graduate schools.

 

Academia as an Unwieldy Vortex

Vortex of Academia

 The safety of academia

In the fall of 2012, I left the comfortableness of the lab in which I had been nestled for 6 years. It was an exciting and terrifying time. I was not going the normal tract for a new Ph.D.; a post-doctoral fellowship. Are we not steered towards a career in academia? I was warned by several professors to make my choice wisely (and for good reason). My wife and I had a life in my town and the thought of uprooting for two to 8 years did not sound appealing. I was very fortunate to take a position as a science writer helping a federal department’s program in biological and environmental research. It was new territory for me, but I knew the opportunity was too great to pass up.

Exactly one year later, I found myself out of work due to reduction in force. I had never gone through such a thing. Those words when they were spoken to me gave me a sort of out-of-body experience, a nightmare really. It took weeks for me to come to grips fully of the immense toll it would take on my family.

Back to the applicant pool

Being a Ph.D. in a mid-sized market is a daunting thing. It seemed as if I was over-qualified or in the running with about 50 other sorry Ph.D.s for each position in which I applied. One part-time position became available as I was hitting the unemployment line as an adjunct professor at a local college. I was teaching ‘Health Science Research’. A great and appealing position if I knew exactly what health science research was. My wife was not as thrilled as I in this opportunity. Who knows, I could land a full-time position soon, I thought. I gladly took the position and kept searching for something permanent and life-sustaining. By early 2014, I had found a hand full of part-time spots to keep us afloat. I was looking several times a day at career sites and every other job portal for the biggest employers in the region. My search had grown to opportunities an hour a way from home. Academia, industry, government; it did not matter to me. I had mouths to feed.

Oh boy, what luck, er tragedy

My adjunct employer asked me to teach additional courses in the summer. However, this schedule overlapped with my wife going back to her position as an elementary school teacher. This meant we would have to pay childcare for a newborn. In other words, we would have to pay the equivalent of another small mortgage monthly for me to work. A catch 22 if ever there was one, but my boss knew my incredible urge to be taken on full-time.

A few weeks after regretfully declining the offer, I received an email on a Sunday morning from my adjunct boss. A faculty member in the Science Department was on life support after a ruptured aneurysm. I was asked to step in (in the middle of the quarter) and teach three additional classes starting the next day. I had no choice but to accept out of respect and duty. The next morning, I found out the faculty member passed away. I couldn’t be happy for my good fortune. How could I? His mother had lost her husband and son within 6 weeks time.

So, here I am stepping into a full-time role with two mid-term exams and a quiz my first week to prepare; not to mention hours of lectures to prepare with no slides to reference from previous quarters. I have not, and will not, complain about my circumstance. I think of his mother and sisters often.

Home Sweet Home

18 months after leaving the world of academia, I find myself thrown back into a forceful vortex. No time to stop and think about ivory walls or effective pedagogy. I’m treading the academic waters for a few more weeks. Going one lecture/class at a time trying to give the students my best efforts, for their sake. Don’t get me wrong, I want to become increasingly effective at teaching my students and getting them curious in biology. Just let me turn in final grades for this quarter first.