Food, Fuel and Pharmacy

Patent Oddities

2010-06-11T12:22:00.000-07:00

One of the most interesting things I have learned about in the course of studying for the patent bar is the amount to which patents are abused. Today I will share with you two of the most rediculous.

The first is a method for exercising cats using a light source.
You may think its cute to watch your cat run and jump for the light but you are infringing on this person's patent. Click here for a gander at the pdf.

Here are the claims from the patent available from the U.S. Patent and Trademark Office.

Method of exercising a cat

What is claimed is:

1. A method of inducing aerobic exercise in an unrestrained cat comprising the steps of:

(a) directing an intense coherent beam of invisible light produced by a hand-held laser apparatus to produce a bright highly-focused pattern of light at the intersection of the beam and an opaque surface, said pattern being of visual interest to a cat; and

(b) selectively redirecting said beam out of the cat's immediate reach to induce said cat to run and chase said beam and pattern of light around an exercise area.

2. The method of claim 1 wherein said bright pattern of light is small in area relative to a paw of the cat.

3. The method of claim 1 wherein said beam remains invisible between said laser and said opaque surface until impinging on said opaque surface.

4. The method of claim 1 wherein step (b) includes sweeping said beam at an angular speed to cause said pattern to move along said opaque surface at a speed in the range of five to twenty-five feet per second.

Kevin T. Amiss and Martin H. Abbott patented this in 1993, which means we only have to wait 3 more years before we can begin legally exercising our cats.

Trolling Patents
The second is the amount that patents are trolled by people with no expertise but look to exploit the complex system where we provide ownership of ideas. Haliburton decided to fight back and patented the process for trolling patents. Check it out here. Thankfully, they have promised to only use their super powers for good.

The inventor and the assignee of this patent have no intention of applying the techniques described herein offensively but instead intend to use the patent defensively to discourage patent trolls and the like from extortionist practices.

Blogging and Disclosure
I have been scarred to post about my coolest science thoughts because it will either start a patent clock or cause me to get scooped, neither of which sound particularly good. Thus proving that in science as in marriage one usually has more to gain from keeping your mouth shut than opening it.

As I study for the upcoming patent bar, I am awed by the seriousness of it all. Though it was not my intention when I began this journey, at the end of next month people could begin coming to me with their hair-brained ideas and request that I patent them, for a reasonable fee. Sure, most patents don't bring money to your bank, but it is quite humbling to think about how easy it is to thoughtlessly destroy someones dreams by forgetting something in the patent application.

After much thought and consideration, I will leave discussions of my scientific ideas to lab notebooks and co-inventors and instead place the spotlight on other scientists who have done some really cool stuff.

Stay on the lookout for articles on exciting new work by Craig Venter and Steven Benner, two of my favorite scientists.

Still too many scientists...

2010-05-16T10:53:00.000-07:00

Apparently, its been like this for quite a while. This letter from Jonathan Katz from 1999 points out that he has "known more people whose lives have been ruined by getting a Ph.D. in physics than by drugs".

Ouch...

Still, I wouldn't be pursuing this career if I didn't think I could beat the odds, come up with something so revolutionary that it will change the world and support a family on it. I have some secret and highly innovative ideas as well as a backup plan.

Knowing that there is a problem is the first step to a solution.

Patent Bar Incoming? To be continued...

2010-04-12T11:10:00.000-07:00

In a new take on future career developments, I am looking into taking the U.S. Patent Registration Exam (USPRE). At a low $150.00, the 3 hour computer based exam from United States Patent and Trademark Office (Prometrics website) gives you the right to act as a Patent Agent, to provide counsel and submit patents.

The exam is "open book" and based on the Manual of Patent Examining Procedure (MPEP).

If you are interested in checking out what it looks like, past exams can be found here and here is the practice exam book that I am planning on picking up to study for it.

I have only slightly toyed around with the idea of going into patent law before this, and I doubt that it will change my longterm career direction. I am pretty set on developing new uses for microorganisms and I expect that it will help me out along the way.

Too Many Graduate Students; Not Enough Jobs

2010-04-01T13:28:00.000-07:00

Today, I offer two articles. The first article is from Scientific American about the current state of the US science and engineering job market, while the second deals with an alternative model to PhD education being explored in China.

Does the U.S. produce too many scientists?
This story by a really eye opening article on how the US overproduces scientific PhD's for the job market and how this bizarre system is maintained through the recruitment of foreign students to fill the ranks.

What I got out of the article is that:
1) US K-12 still produces some of the best graduates in the world. There are some big gaping holes in the public education system that merit fixing, but we should acknowledge that it still produces some really good students.
2) Those students who want to make money don't go into science.
3) Those that do go on to graduate school in science join a grant funding system which supports lots of cheap labor in the form of graduate students and "temporary" postdocs. Then when they graduate with PhD's and want to start their own labs, they discover that there are way too many PhD's for the number of career jobs available.
4) One solution is to switch funding from temporary postdoc's to longterm staff scientist positions. Another is to cap the number of foreign graduate students who are admitted to study in the US and make the cap respective of the market.

I don't feel like I know enough to comment on policy, but I am already weighing options for PhD work and I haven't even started grad school.

Do scientists really need a PhD?
BGI, a Chinese genomics institute doesn't think. The suggested model would be to jump into a research project right out of college without the typical PhD educational experience. While I may be a bit biased, my three years of lab tech work seem to be very similar to what PhD student would go through, minus the required classes and grades. While I look forward to being the first PhD in my family, I truly doubt that the letters, by themselves, will make me a better scientist. I believe that it is the hard work, scientific problem solving and long discussions with colleagues are what make the scientist.

My Future at the University of Texas at Austin

2010-03-16T10:05:00.000-07:00

Its official, I will be entering UT's Cell and Molecular Biology Graduate Program this Fall with the singular goal of getting a PhD in four to five years, instead of the five to seven which seems far too common these days. There is more than enough time to smell the roses after graduate school is done, my first priority is gaining the skills and developing some IP that will provide an upwardly mobile career for myself and material funds to provide for my family.

The graduate life begins by rotating in three to four labs. These rotations are 11-weeks long and give you a general sense of what its like to work in those labs. I am fairly certain which labs I want to work in after interviewing with the Professors during the recruiting event.

Hal Alper - Chemical Engineering

Hung-wen (Ben) Liu - Medicinal Chemistry

Jennifer Maynard - Chemical Engineering

In addition to graduating "early", I intend to acquire outside funding to establish myself as "fundable" and gain practice writing the grants which will be a staple of an academic career. So far, I have applied for the National Science Foundation Graduate Research Fellowship, and hope to hear back from them in a month or two. With Mr. Obama increasing the funds for those fellowships, it seems well worth the effort to apply for them every year that I am eligible. There is also the Hertz Foundation and probably many more that I haven't looked into yet.

Science Fiction Writing: Something that I have been toying with for years has been writing science fiction. SciFi works, such as Star Trek, Jurassic Park and Heinlein all helped shape my interest in doing the hard science work to make the impossible possible. It is also possible to have a conversation with the public about issues too difficult to discuss directly through the medium of books and movies. I foresee some very serious biological issues which will confound non-scientific morale educators and scientists alike to resolve. While I don't intend to solve these problems by writing, I think people can grapple with their feelings on human cloning easier by watching Bladerunner (or Southpark for that matter) than when they are watching Cable News.

I once heard that Michael Crichton wrote ER while in med school. While I don't claim to be his caliber of writer (yet), it has convinced me to keep my eyes and ears open and the fingers tapping on the keyboard.

Lonnie Ingram: Engineering E. Coli for Fuels and Chemicals @UT 2/24/2010

2010-03-12T11:51:00.000-08:00

Two weeks ago, Lonnie Ingram came and gave a talk here and I had a chance to take some notes which I will share with all of you as well as some of my thoughts.

Introductions...
Most fuel in the US is produced domestically. However we still import lots of oil for fuel and coproducts (like solvents).

Biomass is used in three processes right now US Whiskey (from corn), Brazillian Rum (from sugar cane) and University of Florida's Tequilla process (from lignocellulose, hexose and pentose aka starchy stuff like switchgrass ).
Production from cellulose requires acid/base pretreatment which creates inhibitors to cellulases. Usually by dropping the starch in a tub of acid or blowing it up. Then you can mix it in with your bacteria or enzymes in the fermenter.

1. Engineering Organisms for increased yields: Zymononas mobilis
By mucking around with this organism they were able to reduce the net energy loss into CO2 making the fermentation process more efficient. Then they eliminated competing reactions and then used increasing biomass as a selection marker for better ethanol production in directed metabolic evolution.

2. Increasing ethanol tolerance, the more the bug can stand the better for production. I don't remember any publication work that he mentioned.

3. Since there are multiple sugars in starchy sources its important to get the most out of them and he talked about the sugar co-utilization of xylose and glucose, and how it can be improved with mutations to methylglyoxal synthase.

4. Deconstruction and inhibitors: by using cellulases they showed how to skip the expensive liquid solid separation and wash steps and just go pretreatment (see above)->fermentation-> purification (getting your liquor out of the gunk). Now they just need to have the bacteria operate at higher temperature and pressure to get the cost down. The three major compounds which are extracted from the starch and function as inhibitors were furfural from hemicellulose (which Quaker Oats produces from corn hulls for use as solvent or in resins), acetic acid and hydroxymethylfurfural.

The first thing they did was look for a furfurol reductase using mutant screening. They found that sulfur relieved some of the furfural inhibition. Eventually discovering CysIJ reductase and that furans inhibit growth by depleting the NADPH pool.

6. Fermentation for co-production:lactic acid is a co-product in fermentation. They worked with a company to produce it for use in poly-lactic acid (PLA) for the production of bioplastic. Pediococcos IdhL. There is a big need for the production of D and L lactic acid to blend for bioplastic production.

7. Succinate is a key building block (on the DOE top 10) and work done by Xueli Zhang looked at improving yields through flipping pathways around to produce succinate from CO2.

He lastly mentioned how to promote synergy in the way plants are setup taking the waste CO2 from the fermentation part of the plant and producing succinate in another, I would expect to see networks like these in the world future biorefineries.

First Gatorade and now cellulosic bioethanol. The University of Florida really knows how to do technology transfer! Its really great to see academics pushing new tech into the private sector. This makes me cautiously optimistic about the chances of taking some tech that I develop as a grad student or postdoc to the market through a startup. I don't have anything yet, but I definitely have some ideas up my sleeve. Mr. Ingram failed to mention his funding sources but the idea of industry working with academics sounds like a good alternative source of research funding from the NIH/NSF.

2010 A Year of Hard Decisions: How to pick the best choice for a graduate program.

2010-02-25T13:30:00.001-08:00

Recruitment Weekends Rock!
This past month has been a bit of a whirlwind for me. From just finishing up my applications to getting invited to visit my top choices for school, its been very rewarding to say the least. I visited UT's Cell and Molecular Biology Program on Jan 28th and 29th. Working in the building where the recruitment events were located was a bonus, as I got to finish up an experiment I was working on during the downtime at the end of the day. The event started off with a mixer at a hotel downtown where the non-local recruits were staying. The next morning we listened to some talks, went to a gigantic poster session and had some interviews with Faculty. The evening was topped off by a formal dinner and "magic show" downtown at Esthers Follies.

They say that everything is bigger in Texas, and the CMB program has over 120+ faculty associated with the program and growing. This is some consolation because even after working, living and breathing research at UT for over seven years, I still met Professors that I have never seen or talked to before. It was a great victory lap feel for me because of my lack of success at getting in last year and my residual envy of the recruits who did.

The Rice Biochemistry and Cell Biology interview was just as great of an experience. First of all, they flew me in on Thursday Feb. 11th and out again on Feb 13th. I know I could have driven but we only have one car and it would have been troublesome. Upon arrival, not only did they put me up in a great hotel, but my suite-mate got snowed in leaving me alone in what had to be 800-1000 sq feet of posh hotel excellence. The next morning I found out that only five recruits made it that weekend. The other two got snowed in. This was a bit of a shocker for me as UT had at least fifty people in attendance. Granted that was for CMB, Biochemistry and Microbiology, but vast difference in scale reminded me of how exclusive the "Texas Ivy" remains. Rice has some truly gifted Faculty. I met with six for interviews and each one seemed like they would make wonderful advisers. To cap the wonderful day Prof. Jonathan Silberg took us out for some of the best Thai food I have eaten.

Those recruiting visits presented a glorious end to the application season.

Invitations to study
I have since received invitations from both programs. This is very exciting news as less than a year ago I was furtively coming up with alternative career paths in the event that I didn't get into graduate school this year. Now, I had the pick of the litter and the hardest part is figuring out which top-ranked research institution will provide the best location for both both of our careers.

How to decide?
1) For those with a "pseudo-two body problem", consultation is absolutely necessary. This doesn't mean convincing or arguing, but a frank and dispassionate discussion with all the information on the table. A conversation devoid of personal desires and only hoping to find the best solution together.
2) Prayer and Meditation help to put things in perspective. There are a few prayers from the Baha'i Writings that really capture what I want better than I ever could.
3) Just roll the dice. We can't see the future and just have to try to make the best choice with the information presented to us.

A Vision of my Career: Finding the Alchemist Stone for the 21st Century

2010-02-09T14:28:00.000-08:00

My favorite alchemist Hennig Brand by Joseph Wright.

These are exciting times for me as I gear up for recruiting weekend Rice and meditate on UT's recruiting event. I am preparing for the upcoming interviews with some of my favorite Professors by reading their papers and figuring out who I am and what I want to do. Today I will share with the entire world (or just those that reads this blog) why I do science and what I hope to accomplish in my career as a researcher.

Once, I dreamed of molecular dynamic simulations and being able to engineering enzymes to order. As I survey the field of protein engineering, I feel that we are in a much better place as far as making enzymes to order than when I first started following it in 2004. Now I feel that the struggle is to take the next step and build pathways to order. Perhaps I am overestimating the power of directed evolution, but I am confident that its only going to get easier.

My current vision of the work that I want to develop over the course of my career is the use of microbes (bacteria and yeasts) as chemical factories. Now we can use molecular cloning tools to copy & paste whatever enzymatic pathways we want into them, requiring only sugar for their augmented metabolism. I can't help but draw a parallel with the famed Alchemist Stone, which was reputed to turn lead into gold. This "alchemist stone of the 21st Century" will be the methodology combining protein and metabolic engineering. Believe it.

In stepwise manner we turn lead (sugar or cheaper carbon sources) into precious gold (i.e. expensive pharmaceuticals and specialty chemicals):

1) We select a production chassis. This will probably be bacteria (E. coli) or yeast (S. cerevisiae).

2) We clone out the production pathway from libraries or other organisms into our chassis.
a) If no enzymes exist for that chemical reaction, protein engineering provides a toolkit such as directed evolution to evolve it from similar enzymes.
b) Computational simulation provides an alternative to directed evolution by making educated guesses about mutations which may produce that activity.

3) Next the pathway must be optimized in the microbe for maximum flux. Techniques for this involve modeling the pathway based on production in intermediates and up-regulating the steps acting as a bottleneck. This can be done one enzyme at a time or using directed evolution.

4) Now that the pathway is in the microbe and producing the most of our "gold" possible we can opt to switch its "lead" to something else which is cheaper (plant biomass, recycled plastic, or even urban refuse) in similar manner as putting the production pathway in.

5) Last we can include a production "switch", in the form of an inducible promoter, that we can turn on to push the microbes to the limit before we spin it all down and collect our hard earned prize.

These microbes can be freezed down, dried out and otherwise sent anywhere for production of your product. Thus technology transfer within a company or between countries is easily facilitated. The final purification may be tricky to get setup at a biochemical plant, but growing microbes is easy and straightforward.

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

2010-02-02T14:43:00.000-08:00

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

2010-01-27T13:03:00.001-08:00

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?

2010-01-22T14:32:00.000-08:00

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"

2010-01-19T10:08:00.000-08:00

(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...

2009-11-06T08:31:00.000-08:00

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...

2009-09-15T09:11:00.001-07:00

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

2009-08-24T07:54:00.001-07:00

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.

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.
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.
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.
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.
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

2009-08-19T09:44:00.000-07:00

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

2009-08-18T13:56:00.000-07:00

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

2009-08-07T09:46:00.001-07:00

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

2009-07-29T14:08:00.000-07:00

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.

2009-07-17T09:40:00.001-07:00

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.