Germs, for lack of a better word, are good. Germs are right. Germs work. Germs clarify, cut through, and capture, the essence of the evolutionary spirit.

To paraphrase a great movie classic, Wall Street. 

I want to change focus a bit, from bacteria benefiting mankind by cleaning up our messes and providing electricity, to another great benefit of bacteria; their pliability. It is very easy to manipulate the genetics of bacteria (see Biohacking). This owes to their genome structure and lack of miles of “junk” DNA. This means scientists can insert genes from one bacterium into a more well-known bacterium, like E. coli, to perform a novel function and, in a way, reverse millions of years of evolution. For example, in 2011, Jay Keasling and his team at the Joint BioEnergy Institute (JBEI) modified E. coli to degrade switchgrass biomass into sugars. Not only that, the E. coli fermented the sugars into gasoline, diesel, or jet fuel without enzyme additives. Think about it; E. coli, a bacterium that colonizes the digestive tracts of mammals, is able to breakdown plant material and directly convert it into fuel. That is amazing. I’m working on an illustration to depict this, so check back. 


From vinegar, a potential cheap energy alternative: Bacterial nanowires Part 1

Energy. We all have it and we all need it on multiple levels. Within our body, energy is stored in a molecular currency that is conserved among all living organisms, adenosine triphosphate, ATP. Of course, you should know that as humans, we require oxygen to live. During our metabolism, hydrogen atoms are divided into their two opposite parts, the proton and electron. The electrons are shuttled through several enzyme complexes while the protons are pumped out of the mitochondrial matrix creating a much greater proton concentration outside than inside. This imbalance is what drives Nature’s smallest rotary motor, ATP synthase. But what about the electrons? Your body has no need for them, energetically speaking so something needs to accept them for the big show to continue. In our case, the acceptor is oxygen. Oxygen accepts the electrons, and the protons that come along to reconstitute the full hydrogen atom, to form water, H2O. A lot of organisms need oxygen for the same reason. However, just as many organisms have no such requirement while some others are afraid of oxygen.

This leads to the question of what accepts the electrons within organisms that don’t have oxygen present? Anaerobic (“no oxygen”) respiration can utilize many different molecules to accept electrons depending upon the genetic capacity of the organism in question. The more genes within a genome that encode enzymes that can coerce compounds to accept electrons, the more options an organism has in regards of what environment they can survive and thrive. If you have kept up with this blog, you know about a group of bacteria that have evolved a variety of strategies to survive in some of the most undesirable environments on (or in) Earth; Geobacter.

Geobacter have been identified in many anaerobic environments including, soil, sediments, wetlands, and even rice paddies. Geobacter are the predominant species in these environments where there is no oxygen and few other choices for electron acceptors. They are very efficient with their energy usage as well as creative in the ways in which they “relieve” themselves of unwanted electrons. In the absence of oxygen, Geobacter have two major methods of removing the reducing power of electrons. The method of choice used depends upon the type of compounds within their environment capable of accepting electrons; soluble or insoluble. Soluble, water dissolving, compounds include many common organic materials such as amino acids and carbohydrates. Uptake of these molecules is possible and necessary. However, not all soluble compounds are easily tolerated by Geobacter including heavy metals. How can Geobacter utilize these electron acceptors if they can’t bring them inside their cell membranes? The answer is by taking the electrons outside the cell through a labyrinth of electron shuttling proteins called cytochromes. Cytochromes, especially the predominant Geobacter type cytochrome c, use prosthetic cofactors like hemes or copper ions to ferry electrons out of the cell to waiting acceptors.

This is where it gets interesting…

What if only insoluble electron acceptors are present? There’s an op for that! Operon that is. Actually, several operons that are active when sources of soluble electron acceptors are very low. Geobacter can synthesize extracellular appendages that can navigate over several cell lengths to find insoluble acceptor compounds including the predominant iron Fe3+ within the subsurface. These appendages called pili are found in many other bacteria. However, there is something a little more special about Geopili, they can conduct electricity. The protein subunits that compose the geopilus have a shorter peptide sequence than the one found in a majority of other pili systems. Also, a few of the cytochromes c proteins that shuttle electrons to the outer membrane of the cell can actual be deposited along the pilus to deliver electrons to waiting acceptors far away from the actual cell itself.

animated bacteria GIF, bacterial nanowire gif
A Geobacter cell protracts pili (black) out into its environment. As it does so, cytochrome c proteins (blue) are deposited upon the pilus for electron transfer to insoluble electron acceptors (brown).

Put #government labs to work on #climatechange – The Washington Post

I want to start by saying I am part of the national labs system. I’m at Oak Ridge National Laboratory and work as a science writer for a small group that publishes for the Office of Biological and Environmental Research within DOE. That being said, I’m still a concerned citizen as well. I want my daughter to experience this planet as I have. This opinion article in the Washington Post by Naomi Oreskes, a professor of history and science studies at the University of California at San Diego, is brilliant and articulate. Straight at the heart of what the Executive Branch can do without going through the cluster f#ck that is Congress. However, as always, it comes down to money and reapportioning funding for the suggested changes in this article would essentially have to go through Congress. Here are the suggestions in the article:

●Alternative energy. The climate problem is fundamentally an energy problem. While strides have been made — by both industry and government — in developing alternative energy sources, renewables still provide only a sliver of the U.S. energy profile. The scale of renewable energy research and development needs to be radically increased.

●Carbon capture and storage. Shale gas development in the United States and Canada is generating jobs and revenue and could substantially decrease our reliance on petroleum. But shale gas is still gas — methane: a fossil fuel that when burned produces carbon dioxide. Large-scale development may exacerbate the climate problem if inexpensive gas undercuts the market for renewables. If, however, shale gas development could be coupled with carbon capture and storage, trapping the carbon dioxide produced, then this resource might be usable without worsening climate change.

●Energy storage. Wind and solar are real sources of energy, but only when the wind blows or the sun shines. Yet many wind and solar projects produce excess capacity that could be used later or elsewhere if it could be stored. Ideas for renewable-energy storage need to be developed and expanded.

●Social obstacles to energy efficiency. Numerous studies show that Americans could cut energy use by 30 percent or more through efficiency measures and save money at the same time. Yet most of us don’t. This is a bit of a mystery for economists; social science research in the laboratory system should be mobilized to figure out why we don’t save energy and money even when we could.

●Climate engineering. Deliberate alteration of the climate to compensate for inadvertent modification is a technically and ethically troubling concept, but it may be one of the only available means to slow climate warming and buy time while other solutions are implemented. Physical scientists should expand their work in this area, and social scientists and humanists should be enlisted to address the ethical dimensions and governance issues.

Curiosity-driven science has not yet provided the solutions to global warming, and universities are not well situated to address a single, overarching problem. Moreover, the president does not have authority over our nation’s universities. But he does have authority over our national laboratory system. The labs have been mobilized before; the time has come to mobilize them again.


The last part (in bold) is a great remark and one I completely agree with. These suggestions should be sent to the White House, perhaps through the petitions website. Are you with me?

Put government labs to work on climate change – The Washington Post.

Using heat from the Earth’s core for energy production

I was looking over the Office of Science (DOE) webpage and found Dr. Brinkman’s presentations page.

I hadn’t noticed this one before; harnessing geothermal source for a novel mass production power plant. The first activity of the Enhanced Geothermal Systems (EGS) are planned for next year.

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