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?

References

(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).

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.

 

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…

Graduate School Does Not Prepare Students to Teach Effectively

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.

What’s the Big Idea?: We Need to Focus on the Big Picture

global warming
Oh, the irony…
Photo credit: Flickr/Vineus

The Big Picture?

This week, the House of Representatives’ Science, Space and Technology Committee unveiled the Frontiers in Innovation, Research, Science and Technology (FIRST) Act. This legislation wants to prioritize the way the National Science Foundation funds projects in life and chemical sciences, computer science, and mathematics based upon how the projects specifically address national needs. To increase the muddling between science and politics, the NSF would be required to justify the projects funded to Congress and how each benefits the national interests. The measure comes as the Republican-controlled House is pressured to cut federal spending and this would filter out projects with no tangible or timely returns. The bill would also limit the NSF from funding projects that already have funding from other federal agencies in an effort to prevent mission creep and double dipping. The bill fails to address how some projects are complex and have components that have benefits at multiple levels.

This legislation is the latest in a long line of efforts the GOP has used to hinder the scientific community from using its internal peer-review process to advance research and development which in turn would lead to the next generations of innovation desperately needed to sustain the United States’ leadership in science and technology. GOP efforts to appease the extremists within their party by slashing spending no matter who is affected are naive and short-sighted to say the least.

Beginning with the powers of the oil and gas industries masquerading as a conservative, grassroots Tea Party movement, conservatives have fought tirelessly to create an absurd climate debate instead of working on a bipartisan effort to ensure the sustainability of our planet. Congressional leaders have used ‘data’ gathered by conservative think tanks and biased institutes to assert the ‘science is still out’ about the man-made cause of climate change. Ultimately, what are their interests, protecting those who fund their elections or protecting…well, the rest of us? Who stands to lose by enacting cap-and-trade, emissions limits, or biofuel standards? The public as a whole? However, who wins if these and other efforts are in place to fortify our environment for future generations?

Also this week, the U.S. Global Change Research Program released the latest National Climate Assessment stating climage change is no longer a future threat. It’s here. Climatologists have sounded the alarm about global warming for over 30 years. Now the science is as solid as diamond and the consensus is strong. It is very apparent Congress will not actively take measures to grant future generations the awesome pleasure of enjoying our national parks as we have or enjoy time on local lakes or rivers. 

If there is something I’ve learned in the past couple weeks, it is the precious time we have with those we love can end at any moment. I cannot help but think what happens when I am gone? What do I leave behind? How can I show my children how much I loved them and wanted the best for them? It certainly is not doing everything possible to ensure I am victorious every election cycle by bowing to fundraisers.

What can we do to help?

 

It is past time to take back the power by electing members of Congress who can see the big picture by looking past this term in office to the selfless good they can do to help us all. The big picture is increasingly heating up as is our atmosphere.