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.

Useful Products Engineered into E. coli “Poop” (Thank Goodness)

I can’t sit back and let the internet become saturated with misleading phrasing regarding by-products genetically engineered into E. coli metabolism. The latest sensation stems from the commercial production of the artificial sweetener aspartame. It was reported this week, well…read it for yourself (notice the language used):

This scientific jargon obfuscates (perhaps deliberately) a truly disturbing process:
1.) ‘Cloned microorganisms’ (which the patent later reveals to be genetically modified E. coli) are cultivated in tanks whose environments are tailored to help them thrive.
2.) The well-fed E. coli cultures defecate the proteins that contain the aspartic acid-phenylalanine amino acid segment needed to make aspartame.
3.) The proteins containing the Asp-Phe segments are ‘harvested’ (i.e. lab assistants collect the bacteria’s feces).
4.) The feces are then treated. This includes a process of methylation (adding an excess of the toxic alcohol, methanol, to the protected dipeptide).

While common sense dictates that this abomination doesn’t belong anywhere near our bodies, the patent’s authors made no secret about their belief that aspartame constitutes a safe and nutritious sweetener:


It was picked up on the UPI under “Science News” with a headline reading:

The use of the words ‘poop’, ‘feces’, ‘defecate’, and ‘excrement’ is truly unfortunate and used to sensationalize the process. Natural News has an agenda, or several agendas. First they are against genetic modifications to living organisms even though almost all discoveries and breakthroughs in modern medicine can be contributed to some form of genetic modification. Second, they are publicly against the use of aspartame in commercial products.

The truth about E. coli ‘poop’

First, E. coli do not ‘poop’ in the sense a human can relate. These are single-celled organisms and are rather leaky to certain molecules naturally. E. coli produce by-products, not poop. Metabolic end products are considered waste to the E. coli cell, but these natural end products include carbon dioxide, hydrogen gas, acetate (vinegar), and water. Their poop doesn’t sound so bad now does it?

The evolution of E. coli ‘poop’

E. coli has been the organism of choice for decades in myriad research areas. Simple genetic modifications like gene deletion and gene insertion are the norm and can easily be performed in a lab. Scientists and doctors have used this technique to engineer novel strains of E. coli that tweaks their metabolism to produce useful products for the general public. One great example occurred in 1978 by Herbert Boyer who inserted the gene for human insulin into E. coli. Recombinant insulin was approved by the FDA in 1982 and is now the source of 70% of the insulin sold today.

Human growth factor is another by-product engineered into E. coli to treat different forms of dwarfism. For hemophiliacs, E. coli are utilized to produce missing clotting factors like tissue plasminogen activator and factor VIII. It should be noted that before producing these therapeutics in E. coli, they were harvested from cadavers. Patients with immunodeficiency can receive recombinant interferon, used to treat viral infections, produced in bacteria.

E. coli and other bacteria are used in other industries as well. They have been modified to produce large amounts of succinate, a precursor for the solvent 1,4-butanediol. It can then be used to make some plastics and even Spandex. E. coli are also used in the production of polyhydroxybutyrate, or PHB, for the production of plastics. E. coli is also used for production of polyamines for synthesis of polyamide plastics.

Over the past decade, a lot of research has taken place in the field of renewable energy. One approach to lessen our dependence on foreign oil is the microbial conversion of cellulosic (non-food) plant material into viable fuels like ethanol and butanol. This task has given E. coli and other microbes ‘poop potential’. Through genetic engineering and synthetic biology techniques, E. coli can produce large amounts of free fatty acids which are one catalytic step away from the same diesel fuel derived from petroleum. E. coli is also engineered to produce precursors for jet fuel.

In this post, I have focused on only one microbe, E. coli, since this was the bacterium sensationalized this week in the press.

Illustration: Synthetic Biology; Turning bacteria poop into a hot commodity

bacteria art, E. coli art, bioenergy, biomass, biodiesel
Illustration showing the concept of E. coli engineered to digest plant cell wall material (green) and produce fatty acids (white) that can be used as diesel as a waste product. The fatty acids shown are actual 3D structures of linoleic acid.

Illustration of a bacterium that poops electricity and can save the world: Geobacter Hi-Res

Geobacter, nanowire, bacteria, bacteria art, science art

Breaking down the wall: Illustration of the cellulosome as an impressive bacterial machine to degrade plants…think Legos

cellulosome, bacteria, bioenergy
Components of a major cellulosome of Clostridium thermocellum

I have heard of the cellulosome for quite some time. It discribes a extracellular ‘factory’ of enzymes some bacteria (or fungi) are equipped with to degrade the components of the plant cell wall. These enzymes are held by a scaffold structure projecting out of the cell. Several bacterial species to date are known to encode some sort of cellulosome. Here, I will focus on a model species, Clostridium thermocellum.  I never really thought twice about cellulosomes until recently when researching for an upcoming project. Now, however, I have a great appreciation and respect for this massive, impressive apparatus.

The backbone of sorts for the cellulosome is the scaffoldin CipA. CipA is a monstrous protein with many domains, most of which necessary to attach the enzymes needed to break down plant cell walls. CipA contains 9 cohesins, domains used to securely allow different proteins to interact. The enzymes ( I will describe soon) contain dockerin domains that interact with cohesins. CipA also contains a carbohydrate binding module (CBM) which allows it to directly interact with cell walls.

Many of the cohesins are used to attach carbohydrate degrading enzymes, usually of two classes: endoglucanases and exoglucanases.  These work in concert to breakdown cellulose and other carbohydrate polymers. Apart from the catalytic portions of these proteins are dockerin, needed to bind to CipA, and other domains like the Ig domain or X domain.

These enzymes ‘fit’ onto the scaffold protein like Legos. This makes them very modular. Now consider other scaffold proteins have a different type of cohesin (cohesin II) that can be used to attach other scaffold proteins thus making polycellulosomes. For example, Cthe_0736 is a scaffold protein with 7 type II cohesins. This means Cthe_0736 can have 6 other scaffold proteins attached to it meaning this polycellulosome could contain up to 63 individual enzymes which is potentially common considering isolated cellulosomes vary in molecular weight considerably.

illustrated bacteria, cellulosome, microbiology
Illustration of a polycellulosome attached to cell (blue) on substrate (brown)
animated bacteria, cellulosome, microbiology, bioenergy
Closer look at the polycellulosome

In a later post, I will go into a little detail on how these cellulosomal enzymes actually are able to degrade anhydrous polymers of carbohydrate.

Artistic take on ethanol-producing yeast


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