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).

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.

 

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.

Earth: This is Our One Shot, Don’t Blow It

Tomorrow morning, early tomorrow morning, my wife and I are heading to the hospital for a scheduled C-section. I’m going to meet my son. Over the next 20 years or so, my duty as a father is to mould and shape him into an honourable and respectable human being. This is something I do not take lightly for it is one of the purest legacies we leave.

I found myself watching Carl Sagan’s Cosmos Episode 13 this evening entitled: Who Speaks for Earth?. I was in awe of the profound and prophetic words and some points stuck with me. First, Sagan spends some time crafting an image of past civilizations with a comparison between the Greeks and Egyptians. With his explanation that Aristotle believed in two groups; Greeks and Barbarians, this concept rationalized the practice of slavery. There was no sense of a collective community to Aristotle. Sagan also explained the city of Alexandria as the first true cosmopolitan city. It was the heartbeat of innovation and discovery. Its library held invaluable volumes detailing observations and methods. It was not until the mob mentality of the religious deemed the library and its possessions as pagan that the library was razed to the delight of local politicians. It was at this point one of the most poignant statements I have ever heard was uttered…

History is full of people who out of fear or ignorance or the lust for power have destroyed treasures of immeasurable value which truly belong to all of us. We must not let it happen again.

Let that sink in….

My first instantaneous thought was of the Koch Brothers. Scientific discoveries do not belong to any one party or country. These discoveries belong to all of us because they tell of our shared kindredship. We are all in this together.

My second thought deals with the conviction Carl Sagan has to calm the rising nuclear storm among world powers, and he does it in blaring subtlety.  He could see the big picture; how all civilization could end within a short, short period of time. Thankfully, these tensions seem to have died down enough that it is not an imminent threat. But, it does remind me a very real, current threat in climate change. Perhaps, this is one reason the Cosmos series was revived.

In my opinion, the threats of climate change are much more dangerous. The outcome would be the same, total destruction, but the impacts are so subtle most don’t catch the trends. Even when all factual evidence points toward environmental collapse in the mid-range future, many do not see it as imminent or requiring even short-term mitigation.

Earth. We were given a beautiful home. Let’s not blow it.

Jumping on the Carl Sagan Bandwagon (And Following the Laws of Physics)

Embarrassingly, I have to admit something. Despite my overwhelming love of science and passion for teaching science to others, I grew up not knowing whom Carl Sagan was. Back story: I grew up in East Tennessee, the son of a mechanic and a bookkeeper. I never even opened one of Sagan’s books until my 30s. I must say, it was my loss.

I have had the privilege of listening to the stories from those who knew Carl Sagan personally. He sounded like such a sweet, endearing person that the world desperately needed and unfortunately still does. By today’s standards, Sagan was a cosmic anomaly harnessing the knowledge from learning, the oration of a great leader, and the passion to spread the wonders of the universe to the masses.

Since the premier of the new production of Cosmos, listening to everyone talk of Sagan makes him sound like a god, but he was something even more great. Carl Sagan was a genuine, compassionate human being. He saw the big picture, even though it is too often clouded by politics and special interests, as what it was; our collective, solitary home among the vast cosmos. Our home has problems that must be addressed and these problems will continue to grow without intervention. Sagan knew a curious, enlightened society could be a force for change.

I wish I had known Carl Sagan, knowing how he has touched the lives of those who encountered him. Neil deGrasse Tyson has had enormous shoes to fill by assuming the role of navigator through the Cosmos. It is our turn to do our part as science communicators to ensure Sagan’s legacy rekindled is not in vain.

Mother Nature’s Chuckle: The Language of the Universe is not English

Miraculous opportunity for self-reflection.

 

There it is. Our home. To us it seems like such a huge place where we will never meet all our neighbors. A place where we live our daily lives consumed with news and opinions from all directions. We work. We play. We do silly stuff like fight wars or think we are the best at this sport or that.

Now look at the picture. Could you spot ‘us’ without the circle? As the dominant species on our planet, we think we are on top. We can explore our Moon. We can travel to our neighbor planet with robots. It is said the human brain is the most complex piece of matter in the known universe.

All Mother Nature can do is chuckle.

As the above image easily shows, it is all about perspective. Our grandeur is self-inflated. Despite the best efforts and actions of us on Earth, Mother Nature will always have the upper hand. She gives us room to explore. She allows us to make strides, great and small. But inevitably, she always reminds us we can not walk confidently on our journey. Stellar threats are all around; invisible until the time of their death in our black or blue sky. Prehistoric mass extinctions to modern day injuries and destruction in Russia last year.

Mother Nature does not speak any of our earthly language. She only speaks the language of the universe. The language we wish to learn through our research and study. The language we long to understand for it will tell us our true history…from the beginning.

On this International Women’s Day, remember, we are all very important to ourselves. However, our great Mother still laughs at us.

 

 

 

Abstract 2.0 Is On: Help Wanted

I have sat on this long enough. It’s not like a have anything else going on right now (except the birth of a son in a  month, syllabus to write, classes to prepare, evaluations to do, data to journal, …). Introducing:

Abstract 2.0

Here are the details presently. I and anyone willing to help will scour the journals of our respective fields and choose those we feel need to be disseminated to the larger public. In a short synopsis (abstract if you will), an overview of the article and why it is important will be written and deposited here. Details will be worked out on how to submit the abstracts in the near future.

Now is the time to act (or later if now is not convenient)!