Therapy lets paralyzed rats walk again; Old News is still Good News

Here is a really cool nature article from back in September, while I was on break from this blog.

Transformation of nonfunctional spinal circuits into functional states after the loss of brain input

And the synopsis from Science Daily.

These rats hat their spines cut to prevent any movement of signals from their brain. Then their walking movement was restored using a combination of electrode stimulation and drugs.

While we aren't quite there at repairing the damage to the spine, by recreating that movement your muscles can retain/rebuild their memory which will be helpful in physical therapy.

As a child, after learning all there was to know about dinosaurs, I moved on to dreaming about making prosthetic limbs. My plans of going into biomedical engineering ended when my parents gave me a book on Genetic Engineering, but I still love to hear about exciting developments for the physically impaired.

Organic versus GMO; An Alternative View

Organic foods are a hot issue.

I love feedback from my ideas. I welcome it. I adore it. On my own I know very little, through talking to other people I can learn a lot.

Today I will introduce some more details on my views on GM/Pesticides vs Local-Organic-Heirloom Crops. I will refer to them as "big-ag" and "little ag" practices owing to the David versus Goliath nature of the current paradigm even though I recognize that organic foods are big business and are not solely produced by small local co-ops. The following is a very brief description of what I see the differences between big ag and little ag models.

Big Ag Practices

• Pesticides and excessive fertilizers which lead to algal blooms
• Genetically Modified Seeds (bigger, faster, stonger but... see my previous entry)
• Whatever Monsanto sends in the mail
• Shipping across the world long before they are ripe
• Super cheap and available at the supermarket up the street
• Mostly lower nutritional content (picked off the vine green and ripens while shipping)

Little Ag Practices

• Creative Farming Techniques which reduce the need for pesticides and fertilizers
• Natural Genetic Variety (protection against pathogens, see potato famine)
• Heirloom seeds
• Shipping across the city or even being picked up from the farm
• Farmers market, Co-Op, or harvested in your own backyard
• Mostly higher nutritional content (picked off the vine ripe)

As the median real-income of the world grows we are going to see a burgeoning middle class which can afford higher quality of food. However, we can't feed all those people with little ag practices. We must blend the two models into something more... sustainable. Interestingly, its the people on the outsides of this middle class that are the major consumers of organic food because they are producing it within their community as they have for generations or because they can afford the better flavor and nutrition which local/organic produce provide.

Ironic isn't it?

There are plenty of people who opine about the terrible direction agriculture has taken and I think there is some value to that. For myself though, I am dubious about the added nutritional and health benefits of organic foods and have a problem paying a lot more for organic food at HEB. However, when I lived near the Wheatsville Co-Op, which sells organic food direct from local farms at a reasonable price, I went there as often as I could. This suggests to me that there is a sweet spot for little ag in our supermarket world we just need to explore different food delivery models.

Thanks for reading, I just wanted to point out that genetically modified foods and big ag aren't the answer to all our food problems.

Cutting US corn subsidies on the other hand...

Monsanto Sharing Genetically Modified Crops with the World?

Now we can all share some tasty GM foods.

Probably the most interesting news during my application time was that Monsanto will be okay with generic versions of their genetically modified crops.

From a recent Economist we can see that they control the vast majority of the GM seed market, which is growing by leaps and bounds. The idea of being able to save and replant the seeds from your crop seems to be an essential part of agriculture which was missing from the GM vision. Sure you can some really persuasive video blogs together to defend your work, but there has been a lot of injustice in the name of pushing GM as well. Perusing the Monsanto wikipedia entry, one can see a veritable laundry list of victims of big ag litigation. One particularly tragic example is that of Kem Ralph, who served 4 months in jail and was forced to pony up $3 million for saving seeds.

I am a huge proponent of Genetically Modified crops, especially for food. They represent the best chance we have of putting those Malthusian prophecies to rest once and for all. However, Monsanto has been the big fish in the small pond of biotech for a long time and owns most of the seed patents. Therefore we can safely blame them for the terrible roll-out of GM food in Europe which turned the EU against it. Now the biotech world has to backpedal fast to get them to accept them as good for public growing and human consumption.

Without further ado, my top 5 list of issues to be addressed for genetically modified foods are:
1) Balancing profitability with social justice - I like the idea of investment over hand-outs but its a delicate thing and should focus on augmenting local communities
2) Biodiversity. Think about how many different strains of bananas are left? Potatoes? Maize? The Irish Potato famine was able to occur because there was only one genotype being produced. Agricultural heritage MUST be preserved or we risk a repeat of history.
3) Lack of proper human testing - Because its not too out there to think of genes that you don't want to eat. What if the oil that lets you grow oranges in the arctic circle or watercress in the sahara also makes you sick. If you aren't doing adequate testing you aren't going to know till its too late.
4) Spread of genes through cross pollination and horizontal gene transfer to other organisms. Once the genes are out there it really isn't possible to control them, regardless of how good the controls are (i.e. Jurassic Park).
5) Big Ag versus Family Farms - The spread of big ag in the U.S. along with their political bargaining power just makes me sick. Following instructions from the IMF/World Bank developing countries focus on developing their agriculture but can't sell it to the developed world because of agricultural subsidies which you can't take off the books because of big ag. GM's have the potential to really push food away from smaller farmers. Ironically, I am a huge fan of "going local" because of the benefit to smaller farms though they usually market as being anti-GM. I will save my subsidy rant for another day though.

If you want to know about more positive stuff from GM crops, check out this great article by Wired.

Applications are done, time to wait and see; The Future of "Food Fuel and Pharmacy"

(Rice Application)
Started: 09:49 PM, September 07, 2009 (PST)
Sent: 07:07 AM, January 14, 2010 (PST)

At long last, I have finished my graduate and fellowship applications.

I started this whole process back in August getting ready for my NSF Graduate Research Proposal. I have gone back and forth on which schools to apply cutting my list of nine potential fellowships and graduate institutions down to one fellowship and two schools. Its been a long six months but its been I think it will be more successful than last year.

1) National Science Foundation Graduate Research Fellowship
2) University of Texas at Austin Cell and Molecular Biology Program
3) Rice University Biochemistry and Cell Biology Graduate Program

UT and Rice are great institutions but what really sold me on these two programs was finding faculty who will help me do the work I want to do. My research interests are like an arrow pointed at one goal: developing a system to generate microbes capable of producing any chemical or biochemical desired. Enzymes provide better tools for chemistry than any synthetic chemist and evolution and replication do the rest of the work. All we need to do is use our "cut & paste" molecular tools to make it happen... or so it would seem to the naive student. I have my whole life ahead of me to solve this problem and I know there is a huge potential for both societal and financial gain. One authors vision of these nascent technologies can be found in the book Islands in the Net by Bruce Sterling in which Mr. Sterling envisions bacteria grown by biotech researchers in super-tankers off the coast of Grenada producing cheap food and pharmaceuticals. You may have just guessed where the title of the blog is from ;) .

Its going to happen. Believe It!

In writing up these applications I enlisted close friends and family for feedback on the essays in which I wrapped up the last 8 years of my life into a bundle of words with the hopes of attracting the attention of the best minds in the world. I will check and see, but if the schools don't mind it I will try to reprint my application essays as they may help the other undergraduates out there looking for ideas on organizing your thoughts.

This process has helped me re-learn how to write persuasively. The one bit of career advice that my Father stressed from when I was six was that the most powerful tool that I have is the persuasive use of the English language and I have to agree. As a scientist, it seems like how well you write about your work is as important as the work you do. I don't think my writing was particularly amazing, but I do feel like it was representative of the work that I did and why I did it, which is all I hoped for.

The Future of "Food, Fuel and Pharmacy"
Starting today, I will update this website on Tuesdays and Fridays with science news articles and my journey through academia and (hopefully) industry as a research scientist. By following me or putting me in your RSS reader you will get to know me and the work that I am passionate about. I see this as a longterm project which I am committed through for at least 2010 and if it goes well than many more years to come.

You can also follow me @TheLeavitt for short and sweet reviews on other peoples general news articles.

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!