Its the little things...

I am still working hard on my applications, but the good news is that I just submitted my NSF Graduate Research Fellowship application and now I just have graduate school's and this plant biology class to worry about.

Lab work is going great! Just got some results that will likely lead to a publication in the next couple months.

My current focus is keeping up my busy tempo and not messing up. Expect more science blog entries mid-late December.

Too Busy...

I apologize for the hiatus. Life has been filled to the brim lately. I started a new project in the lab (hot stuff which will hopefully turn into a paper as soon as I get some results) as well as starting up my graduate applications for Fall 2010 and taking an undergraduate class for some GPA boosting.

I will be finalizing the list of schools this week and will begin sharing all the juicy auto-biographical details about my journey from kitchen chemist to synthetic biologist as I straighten out my application statements.

More science to come, I promise. Until then I leave you with a great article by The Economist on BioHacking.

How to turn your clunker into a biodiesel roadster

If you haven't seen Fuel, you should check it out. I missed it while they were showing the movie in Austin but the trailer alone is great inspiration.

Here is a brief how-to on doing a biodiesel conversion for your diesel truck/car/mobile home.
I pulled from a number of internet sources and have no practical experience, but if you are thinking about running your diesel truck/car on veggie oil instead of that Texas Tea you might want to check the process out here first.

Things to be careful of:
-Be sure to convert your engine with a proper kit. The oil will act as a solvent to the rubber seals (on predominantly older models).
-Filter your oil to avoid food particles building up in the engine.
-Start up and turn off your vehicle with regular petroleum diesel to keep the lines clean of oil gunk.
-Use/Install a secondary fuel tank for your Straight Vegetable Oil (SVO).

For help getting started, you should checkout Greasecar.com. Its a wonderful site with lots of help for biofuel enthusiasts as well as selling the conversion kits and other parts at reasonable prices.


The following instructions are from EHow.com. Thanks Lilia Scott for writing it up better than I could.

1. Start with a modern diesel engine. Nearly any newer diesel engine can be converted to run on vegetable oil as long as it doesn’t have rubber seals in its fuel system (only older diesels use rubber seals). The rubber seals will deteriorate when exposed to vegetable oil over time because vegetable oil acts as a solvent.

2. Install a vegetable oil fuel conversion kit or have a mechanic do it. You should keep the original gas tank to hold regular diesel or biodiesel fuel for cold weather. Install a second tank for vegetable oil; these sometimes go in the trunk. The conversion kit should include hoses from the car's radiator to the vegetable oil tank to heat the oil via a heat exchanger before it enters the final fuel filter and injectors inside the engine compartment.

3. Get vegetable oil. New vegetable oil is easiest to acquire but very expensive. Restaurants will often give you their waste oil for free. Chinese and Japanese restaurants are best because their oils comes out cleanest. The oil should be amber in color. Oil from other types of restaurants may also be suitable but could require more filtering to remove food particles. You will need a few containers for transferring the oil from the source to your filtering destination. The five gallon jugs that the restaurants receive the fresh oil in work fine. Restaurants are usually happy to give you these containers since it saves them disposal fees.

4. Filter the oil. Use filter bags that are rated to 0.5 microns thick. To increase the life of your filter bags, first allow the oil to sit in a barrel for about a week to let particulate matter settle to the bottom. Then, pump or scoop the oil into a filter bag suspended above a fresh empty barrel from the top of the barrel (since most of the food particles matter and possible water is at the bottom). Start your engine using regular diesel or biodiesel fuel from the normal gas tank. Once the engine and vegetable oil are warm (after about 15 minutes depending on weather), switch to allow the vegetable oil to flow into the fuel source.

5. Switch back to diesel or biodiesel a few minutes before you stop your engine for any time (about 10 minutes depending on the temperature) to make sure the vegetable oil is purged from the fuel line and injectors so that they don't become clogged when the engine cools.

In fact diesel engines were originally designed so that they could be run on Vegetable Oil. Thanks Rudy for thinking ahead!

Native American Biofuel

This great article in the NYTimes showcases the synergistic potential for next generation biofuels to work with existing fuel sources. Like Craig Venters partnership with Exxon that I highlighted earlier, feeding algae waste CO2 from industrial waste streams seems like a great way to help out chemical and power companies reduce waste as we move towards a higher cost of polluting via a proposed cap and trade system one way or another.

These algal systems will allow companies to cut down on emissions as well as generating some profitable by-products similar to using industrial fly-ash to produce drywall for housing.

As far as Solix’s AGS^TM Technology, I am not a believer. It seems to refer to the housing unit for the algae and I would place my bets that Exxon and Venter will have some equally good aquaculture units as well as some really exciting strains of algae to work with.

Tech aside, the business model that the Ute Indians are working with seems a refreshing combination of ethics and economics. Taking the long view is better for everyone.

Wooden Bones

I just started up a new project in the lab and my current one has been heating up, so I haven't been as diligent as I would like to be in pushing out my weekly entry. However, I have rededicated myself to learning Chinese as a second language and am happily committed to at least an hour a day to make it stick. As a consolation prize, I will be getting out a couple this week so stay tuned.

One thing that jumped out in the news to me. The Discovery Channel had an article on making a bone implant from wood, how cool is that?

The work was published in Journal of Materials Chemistry by Anna Tampieri at the Institute of Science and Technology for Ceramics, Faenza. They were able to make a bone-mimetic material out of wood for use in supporting bones post-surgery. "The material keeps its original microstructure, exploiting the unique architectural properties of the wood's cellular make-up, explains Tampieri. This means cells and blood vessels can grow through the structure and incorporate it into the original bone." (JoMC article here). How cool is that? I wonder how long it will be before someone figures out how to grow nerve fibers and muscles around it a bio-prosthetic.

Red Beard, eat your heart out!

The Synthetic Life

How DNA functions as information
“I view DNA as an analog information system, and I hope to convince you in fact that it is absolutely the software of life.” - Craig Venter (via John Tierney)

DNA is the blueprint of life. DNA is transcribed into RNA which are translated into proteins which are the movers and shakers of the biology world (with some RNA help?). By analyzing your genome Doctors can weigh your risk for disease and in a few years will probably be able to guess your shoe size and accuracy of your jump shot. By looking into lots of genomes we can map out evolutionary histories and to some extent make predictions.

But the real clincher for me is that DNA is such a portable platform (to borrow some software terminology) you can take a gene from a tomato and clone it into a bacterium and vice versa. There has been a push lately to codify these genetic building blocks in a rational way, so that it will be easier to use these BioBricks. This codification is both a cause and an effect of the growing role that industry is playing in the development of genomic technology. Academic Biology has left us with a very complicated library of biological information. Genbank has done a great job of cataloging these resources, but it is just a start.
We need the Web 2.0/Facebook approach for Genomics, Proteomics and for all the other "omics" which will be coming in the next century. One thing is for sure, it would make annotating GO info easier.

For more information on Craig Venter and George Church's talks about the future of synthetic biology and its impact on humanity go here. And for the record I was giddy as a school-girl when I read about Sorcerer II's voyage.

What is Synthetic Biology?

• Synthetic biology refers to both:
  • the design and fabrication of biological components and systems that do not already exist in the natural world
  • the re-design and fabrication of existing biological systems.

from Syntheticbiology.org a marvelous portal, which along with Open Wet Ware constitute an online community committed to connecting this brand new field with the world.

How do we manage this resource?

As anyone who has seen GATACA knows, this information is a double-edged sword. Its all well and good that you know you have an 45% chance of getting toe-cancer in 5 years, but what if your insurance company gets to see it too? Should they put you on a list to get dropped like a bad habit at the first opportunity or stick it out even though it is bad business? We in America have had a devil of a time changing one iota of our healthcare system and I will be honest, I don't see this looking good in the 20-50 year spectrum.

Germany and Synthetic Biology

"The DFG (which funds university research), the German Academy of Sciences Leopoldina and the German Academy of Science and Engineering argue in a 27 July report that synthetic biology has great value to society — as long as the field's expansion is balanced with ethical debate." - Nature.

I couldn't seem to find the actual press release in English, but going by the article on Nature's website, Germany is taking a big lead in raising awareness of the field which has the potential to bring both helpful and hurtful technology into the world. I am all for a deeper discussion of the implications that research has. We are beyond the flower garden where all research is good and golden and are steadily moving into the thorny bushes of an uncertain future.

I intend to give the ethical issues greater focus in future articles and will only suggest that society will always have a mixed opinions and pray that a few opinionated people don't make my job doing proper research that much harder.

What is my angle?
My personal interest in Synthetic Biology comes from my belief that the tools of molecular biology can unlock a potential of organisms to remake them as we chose. By exploring this potential we will find solutions to many if not all of the worlds earthly ills. Rigorous understanding of biological systems will allow for greater uses of microbes use of as vectors in production of pharmaceuticals and remediation of toxic spills as we are able to use a modular chassis and just swap what the bugs eat up or spit out. Truly the 21st century alchemist stone.

Some hot topics in the coming years...

Fuel
As my last article talked about, we are getting some really cool and innovative solutions coming from biologists to solve the problem of getting clean fuel to the masses. I suspect that the 21st century will deliver a cornucopia of options with technology being adopted by region. For example East Texas would be able to generate enough biodiesel/bioethanol to fuel itself while West Texas can probably survive on wind power.

Clean Air
The prominent use of aquaculture for biofuel producing algae means that waste CO2 will soon be a commodity.

Drinking Water
I am not one for Malthusian arguments. They appear in times of great cynicism showing forth great maths to implicate the death of humanity because of its fertility. However, it looks like drinking water may be a premium in the next century for large parts of the world and finding a way to de-salinize or purify dirty water will be of great use to humanity. I can see some biological solutions to this, but I think mundane engineering will be the ones to solve this problem.

Food
One could imagine symbiotic bacteria in our stomachs adding digestive power to our bowels letting us consume fibrous plant matter by chewing the cud (just like cows do). Or growing bacteria or yeast in vats to produce tasty scop, like in Islands in the Net.

Shelter
I dream of planting house-trees. Think about it, if you can program the instructions for growing into a house into a little seedling all you need to do is find the right soil and plenty of rain.

Cellulosic Ethanol versus Biodiesel

When I was first introduced to Biofuel it was laid out in a plan for communities to generate ethanol from grass clippings (albeit some fancy grass). I loved the idea, communities processing their own waste into fuel. However, as companies have tried to scale up production, bioethanol has lost its luster. As a fuel source it has less energy than gasoline and production from food sources (corn) requires the use of gasoline, water, fertilizer and other inputs that lower the energetic profit, as well as purported environmental benefits. There have also been some embarrassing articles published noting that the dubious energy benefit is just a big farming subsidy scam. It could work, in theory, but we aren't there yet with the efficiency.

To make alchohol based technology a real option, one must look up the energetic food chain at larger hydrocarbons like butanol. And the big issue of competing with food crops? Chew up some waste products, like corn stover, with cellulytic bacteria and then use that sugar as an input for higher alchohol fermentation. Interestingly, the Soviet Union did a lot of research into making Acetone/Butanol/Ethanol fermentation from agricultural waste. ABE has been historically used in gunpowder and cordite manufactuing. BP has invested in cellulosic based butanolic fermentation.

Biodiesel is manufactured by a different process and uses oil as the initial energy source. People have been running cars on spent fry oil for years because the chemistry is so simple you can do it in your backyard. However, as we found out not too long ago, the push for fuel can have a negative effect when it comes at the expense of food. However, if one were able to convert non-arable land into producing oils neccessary for biodiesel, perhaps using algal culture, they would have a real winner for both environmental, economics and with some protection for food rights. Exxon-Mobil has backed Craig Venter's Sythetic Genomics in producing algal derived biodiesel.

Both technologies have great potential and I will be following closely at their development by the Big Energy as well as the little guys like Mascoma.

Welcome to my little slice of the internet, introductions are in order.

My name is John Leavitt and I live and work in Austin, Tx. I graduated from the University of Texas at Austin in May 2007 with a degree in Biochemistry with a specialty in computational work. I worked in the Lloyd Lab for three of my five undergraduate years contributing to this publication and to these Arabidopsis mapping populations being submitted to the Arabidopsis Stock Center as part of the Arabidopsis 2010 Program. Since graduating I joined the Krug lab as a research tech (who also takes care of ordering, budgets and a few other administrative things) and I have been working on exciting work making anti-viral drugs.

I am starting this blog (long after the web 2.0 blog craze has passed) with a few very specific goals in mind.

1) Share cool science discoveries with the world with a minimum of technical jargon. Sure there are some big press releases (Human Genome Project, HPV-Vaccine, etc.) but there is a lot of stuff that doesn't get reported.
2) Explore the literature. I will be writing up some funding applications in the Fall and I want to be on top of what other people have already done so I don't reinvent the wheel.
3) Get my name out there. Feel free to check out my resume.

The plan is for science updates on Monday and current events spread throughout the week. Let me know what you think in the comments.