Soil: an under-appreciated dynamic consortium of communities.

Quick fact: the amount of data generated by analyzing the genetic make-up of 1 gram of soil would surpass the total for the entire Human Genome Project. That is because a gram of soil may contain between 2,000 and 18,000 different genomes comprised within roughly 40,000,000 to 2,000,000,000 bacteria cells (1) and (2). Soil; we all walk on it, but do we ever think about what might be lurking in it? My daughter does, for instance, because she looks for tiny black snails to bring into our house and put in potted plants. However, I’m referring to things much smaller and much more influential to the overall ecosystem. Bacteria and fungi have mostly beneficial impacts on the lives of plants, but we know only a fraction of a fraction of the total species present. Many of us think of soil as dirt; dry and inorganic, but soil is a dynamic matrix of clay, sand, and silt particles with a mix of decomposing matter and living organisms. The surfaces of these particles make good niches for bacteria to live if they can survive the extreme variation in water and nutrient availability due to the wet/dry cycle.

Soil is a vast reserve of organic carbon, but only a fraction is usable due to decomposition of most carbon into hummus. So, bacteria and other microorganisms are in eternal competition with each other for precious nutrients in their microenvironments. This makes life arduous for soil organisms that are loners or isolated from good sources of nutrients. This is one reason the root zones of plants are like retirement communities to bacteria and fungi; and the plants know it.

Plants are like shipwrecked sailors stranded on a desert island. They have no where to go if conditions change. To help themselves out, they recruit bacteria and fungi to live on, or within, their roots by excreting valuable nutrients into the soil. Surrounding microorganisms take to this like sharks to blood which is what the plants want and need. These bacteria and fungi offer several advantages to plants. First, they can simply take up space; space that plant pathogens would like to inhabit. On top of this, the good bacteria can readily produce antibiotics to kill off any pathogens that might kill their food source. Second, many of these bacteria have the genetic machinery to produce a class of plant hormones called auxins, derivatives of the amino acid tryptophan. Auxin is like human growth hormone. When the bacteria excrete auxin, the plants take it in because it is a cue to increase water and nutrient uptake. So, plants increase nutrient uptake, become healthier and bigger, and by default excrete larger amounts of nutrients for the bacteria. Genius.

The third reason plants attract bacteria is because plants have a big problem; they can’t make useful sources of nitrogen out of thin air. Luckily, many soil bacteria can, and it’s called nitrogen fixation. These bacteria are able to take nitrogen gas from the air and convert it into a form useful to both plant and bacterium: ammonium. This is an energetically expensive process for the bacterial cell. So, in order to make it as easy as possible on the bacteria, plants will protect the cells from nitrogen fixation inhibitors like oxygen and provide essential carbon in the form of amino acids. For this to happen, the bacterial cell literally crawls inside the root cell and becomes a bacteroid encapsulated within a special structure, a nodule, and ultimately becoming an endosymbiont.

And you thought only mammals had beneficial internal bacterial ecosystems. Just like humans, plants would be in a sorry state if it were not for the bacteria that they associate with. I haven’t even touched upon the benefits of fungi, but I’m definitely not a fungal expert. Any takers?


(1) How Deep Is Soil? Daniel D. Richter and Daniel Markewitz BioScience , Vol. 45, No. 9 (Oct., 1995), pp. 600-609

(2) Paul, E. A. & Clark, F. E. Soil microbiology and biochemistry (Academic Press, San Diego,1989).

How Old Are You?


My 4 year old daughter could tell you how old she is even though her concept of time is essentially nonexistent. She can’t wait to be “big”, which in her mind is 5 years old. However, the rest of us are not much better at answering the question about how old we are. Yes, we are correct about our legally recognized age, but we are way off on our natural age.

We’re all the same age…really old

Atomic level

Since everything is made up of matter, we all consist of atoms. These atoms all come together to make us who we are, but my daughters atoms are not 4 years old or even 4 billion years old. At some point shortly after the big bang, atoms came together thus forming the different elements (think periodic chart). Here we are 13.7 billion years later; all of us made of the same elements. This makes me shake my head when I think of nations going to war. We’re all made of the same elements, same matter. It doesn’t seem natural. With this argument, we are all really old at about 13.7 billion years old.

We’re all about the same age…really young

Cellular level

Humans consist of around 10 trillion human cells (excluding the 100 trillion microbial cells). These cells have a turnover rate that suggests each human consists of entirely different cells every 7 years. With this argument, we are all pretty young with no one older than 7 years old.

We’re all rentals…really short-lived
Since we’re all made up of the same atoms and these atoms have essentially been around forever, they have been used by other matter before us. And, most certainly, they will be used by matter long after we as humans are gone. Mother Nature sees us as atomic renters, but definitely not rent-to-own.

We’re all tenants…really big compared to our landlords
Something else I have been thinking about for a while now; almost everything we see or touch is completely covered with a thin layer of life, i.e. bacteria. They cover us. They cover our loved ones. They cover our…everything! Also, they have been around a lot longer than we have as species. We are just using the same space they are. Heck, we are a space they live! So, in this sense, they are allowing us to use this space as tenants. They are very nice landlords, too. Consider all the benefits we receive from their generosity (think microbiome).

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.


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 We all know Pitt as an actor, however, we know him just as well for his charity work through the Jolie-Pitt Foundation. 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?

STEM Interest: How Can I Help?

I have wanted to write something for quite a while but have not had the proper inspiration (or motivation). When in doubt, go with your recurring thoughts. For me, this includes interest in the STEM fields locally or globally via the internet.


I recently did a search for local STEM organizations that I could volunteer my time or efforts. Knoxville, however, is not really considered a STEM-Mecca. Actually, I did not find a single NPO focusing on science. This was not a huge shock, but it was a huge disappointment. I know I am not the only Ph.D.-strapped person in the area who could potentially help spread science literacy or interests.


In graduate school, my major professor did talks at local middle schools that we gladly went to so these students could see what an actual scientist looked like. We were an eclectic bunch just like the science community itself. We could tell the students enjoyed and appreciated our visits, and hopefully some of them will pursue a career in a STEM field. I now try to fuel interest in my own undergraduate classroom for my students. I’m not satisfied with my current reach and would love the opportunity to expand it. The best way to a future with progress and prosperity is through a logical and literate society.


I do my little blog with my little graphics and illustrations. What else can I do? I need to channel my passions for spreading the science in a focused and steady way. So, I need your help: help me help others.

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.


Technology Education for Students Is Essential in Creating a Future STEM Workforce, and It Starts With Educating Teachers | Felix W. Ortiz III

This truly is a growing concern and rightly so:

Technology Education for Students Is Essential in Creating a Future STEM Workforce, and It Starts With Educating Teachers | Felix W. Ortiz III.

A Career Change is Quite Literally a Dream Changer

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…