Wednesday, January 30, 2008

Nothing Much Going On

I'm been silent for awhile. There just hasn't been anything really newsworthy or significant to write about. Hamilton Smith has synthesized the first whole bacterial genome. This is the next to last step in creating a tailer made microbe. The news touts it as creating synthetic life, but that's hype. It's just an expensive and fancy way to genetically engineer a microbe. There are simpler and cheaper ways to genetically engineer a bacterium. That isn't the hurdle though. The hurdle is getting the organism approved for environmental release. We've had genetically engineered organisms that could eat oil spills, but those organisms won't be used in the creators' lifetimes because of fear. Still, what Hamilton Smith and his team have done is quite a feat. They have already proved they can transform a whole genome into a bacterium and then select for the segregants (those bacteria carrying the new genome). So, likely, they've already transformed the new genome into Mycoplasma. I'd be more impressed if they heavily modified a genome and put it into something like E. coli or Streptomycetes.


Hi John

Over the oil spill eating organisms is the fear that these organisms are:

- new, thus requiring a long experimental cycle?

- will spread and "eat" good oil out of vehicles or oil reserves

- or will mutate and cause unforeseen damage?


The organism I am talking about was a Pseudomonas species of bacterium. It could already subsist on crude oil, but it was given an extra metabolic pathway to allow it to consume cyclic phenols if I remember correctly. It would thus eat more of an oil spill. Since it was never allowed to be released in the wild, scientists searched for natural organisms from oil reservoirs and contaminated soils. They try to grow these natural bacteria and then spray them on oil spills. To answer your question though, crude oil is a geochemical. If the Earth makes it, life will find a way to eat it. Those organisms already exist, but they can't eat pure hydrocarbons. Nothing will grow on honey because the honey will suck the water out of it because of osmotic pressure. Similarly, nothing will grow in a refined tank of gasoline or any hydrocarbon unless that tank contains contaminants of other nutrients or water. Organisms require carbon, nitrogen, phosphorous, water and other trace elements to live. This is why they spray detergents and fertilizer on oil spills to promote the growth of existing microorganisms that can eat the oil. The detergent increases the surface area of the oil allowing more microbes to eat it. As to your fear that they'd eat oil in oil reservoirs, they already do. They've found extremophiles that subsist on the crude oil in oil reservoirs. Scientists have pumped molasses into oil reservoirs in an attempt to promote the growth of these organisms in the hopes that the gas they produce will raise the reservoir pressure allowing more oil to be recovered.I also believe that jet fuel has to be treated with a fungicide to prevent the growth of some fungus or microbe that likes kerosene.( Germans metabolically engineered a microbe to consume modern firearm propellants. It was necessary because they had to dispose of all the leftover munitions from East Germany after the Berlin Wall came down. Since it was an industrial operation though, they were encouraged rather than discouraged. I searched Google using "microbial degradation East German munitions" and found loads of references to bioremediation of contaminated groundwater and soils. There was one paper from 2003 that used a Penicillium species to breakdown RDX. Unfortunately, I can't find any reference to the modern gunpowder eating microbe though I know it exists.
Hi John, Came here from George's! This is quite a scientific blog indeed, blows my mind! But yet I like your introduction - Looking for God and purpose in life. Without searching, I found the two.
Nice meeting you here.
Dear Swahilya,

Then you are blessed! Everyone is on a different path spiritually. And welcome! This blog is a crude reflection of me. It's a mixture of opinions, facts, comments of what interests me in the moment. It's part science education, part spiritual, part IT, part military history, and part information security. Please look over the links to the right. I hope you find this blog useful.

Thanks for the oil bio explanation John.

"metabolically engineered a microbe to consume modern firearm propellants" sounds nifty.

Could be used as a way to bring peace or as a new weapon to give one's side the advantage.

It wouldn't work quickly or more likely microbes are already eating firearm munitions which is why munitions have shelf lives in the first place due to chemical and microbial degradation of the propellants. Most likely, microbial degradation would happen quicker in a humid environment, but since cartridges are hermetically sealed, likely chemical oxidation is the main cause of munitions going bad. So, the German microbes to be really effective would have to have some way to collect moisture from the air to help them survive in such a dry environment. Remember what I said about honey. Sugar seldom goes bad because it's so dry. Nice idea but it needs more development. :)
Thanks John, Actually you know, when I spend just a bit little time more reading this post, I am able to understand! When science is bored through (as in deep boring the ground)one gets to the spirit of it disappearing in atoms, molecules, sub-atomic particles and quarks! And that's what everybody calls God, Spirit or the innumerable names there are to it.
Thanks. (May keep in touch at
Think of Science as a methodology to measure and test the part of God we can observe. Testing or discovering Nature and its laws is another form of experiencing a facet of God. And, at the microscopic level, we find that emptiness is form and form is emptiness - what Buddhists have known for 2500 years. But in the end, yes, everything is sacred.
Yes, now it is even clearer to me!
Thank you.
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