Sunday, October 11, 2009

Global Dominance

As I was thinning out my strawberry plants yesterday, it occurred to me once again that everyone really is trying to take over the earth and strawberry plants may well be on their way to success.  The resistance genes I work on have already done it, though the ones I have created in the lab haven't (thankfully, copious amounts of bleach seem to prevent that).  

In my own little way, I am also trying to take over the earth.   I have had a little success because medical doctors now have respect for phylogenetics, and they didn't when I started.  (I wasn't alone in that effort, so I can't take all of the credit.) Using phylogenetics to study disease is a pretty universally accepted practice and lot's of doctors cite my papers.  Does that equal global dominance?  Well, if it does, I am not sure why it is such a desirable thing...and yet, I am still persisting at it.  Maybe it's just what we do as living organisms.

My next attempt at global dominance is to get some good microbial pop-gen theory developed and universally accepted.  If the number of manuscripts I have planned actually get published, it could happen. Ha! Ha! Ha!  Just remember you were warned and don't be too afraid in the meantime.....  I'll be kind and generous (with my enormous UC furlough-reduced professor's income) if it ever does happen.

Saturday, October 3, 2009

Synthetic Biology

A recent article in The New Yorker entitled "A Life of its Own" included the following quotes about synthetic biology: 
"For the first time God has competition." -Nature 2007 
                               and 
"What if we could liberate ourselves from the tyranny of evolution by being able to design our own offspring?" -Drew Endy

Synthetic biology is the science of engineering organisms to produce something or do something new.  Genes from different organisms are brought together in a single organism to perform some new function.

The upshot of this article seems to be that the practitioners of synthetic biology can do a better job at creating/designing/selecting life than either God or evolution.  That seems pretty arrogant to me...even for professors at MIT and Stanford.  

As an evolutionary biologist who works at the fringes of synthetic biology by engineering and accelerating the evolution of antibiotic resistance genes, I am very impressed by the potential of synthetic biology.  I attended a talk a couple of years ago amorphadiene, which is a precursor to artemisinin,  an excellent antimalarial drug produced by plants.  While this drug is affordable in developed nations, it is too expensive at 10 cents per dose for most Africans to afford.  Jay Keasling was able to cobble together the genes and pathways necessary to get bacteria and yeast to produce amorphadiene.  This has made the drug artemisinin affordable in Africa.  

 I think that this project is a small demonstration of the potential of this type of science.  However, it is not the only demonstration of this type of science.  Organisms have been cobbling together genes and pathways as long as they have existed.  For example simple comparison of the genomes of most strains of E. coli with strain O157:H7 shows how different genes from viruses and pathogens have been assembled in O157:H7 to make it capable of invading and taking control of the cells of the human digestive tract.  On a more positive note, the bacteria that are resistant to toxins and and able to help in bioremediation efforts often have numerous genes assembled from many organisms.

While I fully support the use of evolutionary tools by scientists to develop technologies that support human interests, I think it is dangerous when humans think that they are superior to natural forces.  Billions of dollars have been spent to develop semisynthetic antibiotics with the thought that man could do a better job creating antibiotics than nature, but resistance to those antibiotics has developed more rapidly in some cases than resistance to naturally produced antibiotics.  

A more worrisome aspect of drastically changing life without evolution is that deleterious effects of combining genes from different organisms can be ameliorated by mutation and selection as a new combination of genes spreads through a population.  When substances are produced synthetically and then distributed throughout populations, their deleterious effects have not necessarily been detected or removed.  It is possible that great harm could come upon large populations through synthetic biology because the purging process of evolution was eliminated.

More disturbing to me than the claim that synthetic biology is better than evolution, is the claim that it is better than God.  When I watched Gattaca in high school, I thought that there was no way that humans would be able to pick the traits that they wanted their children to have. I thought that the movie was simple an overly imaginative writer going a little wild with sci-fi.   However, the technologies that are necessary to custom build children exist now.  They are not affordable or practical, but at some point they might be.  It seems that artists and writers inspire scientists with wild futuristic ideas and that scientists make those ideas become reality.    In a small way a scientist becomes a god in his or her laboratory....growing life and destroying it...proclaiming what is good and what isn't.  However, as scientists do this, they are often dwelling within the confines of relatively small offices and labs where most of the problems that confront society don't exist.  To most scientists the perception and purpose of God is limited to the first two chapters of Genesis where the creation of the earth is described.  If the only purpose of God is to create, then I wonder why the rest of the Bible (not to mention other scriptural texts) exists.  

I guess that there are a number of people whose knowledge of the scriptures is greater than scientists because they have expanded their scriptural repertoire to include a verse of John that reads:  "Truly, truly, I say to you, unless one is born again, he cannot see the kingdom of God." (John 3:3).  Those individuals go to war with scientists about whether God and evolution are real and I worry that ethical decisions about how the organisms with synthetically engineered functions or characteristics should be used and treated are given less and less consideration.  Many people perceive cloned organisms as mindless zombies, when, in fact, a cloned human would be a real individual with and independent mind and emotions. If the time comes when human cloning is performed, I worry that those individuals might not be treated as well as non-cloned people. When scientists start declaring that their works are greater than God and evolution, I worry that the morals relevant in their own small universes might not be sufficient for society.  I find myself hoping that they are not the ones who will be making the ethical decisions about what should be done with their work.

Monday, September 28, 2009

All Better!

My dad is out of the hospital! He has returned to life as normal and he sounds good on the phone. I am going to visit my parents this weekend and I can't wait. It is nice to once again have the peaceful sense that all is well.

I am slightly tempted to digress into how Chlamydia pneumoniae (This is not the type that is sexually transmitted. It's airborne.) contributes to atherosclerosis, but I am in too good of spirits to digress into such dismal topics.

Friday, September 25, 2009

Xanthomonas campestris

Mainly I have always know X. campestris as a plant pathogen that sometimes harbors resistance genes I'd like to study. It has taken on a new role in my life though, and is currently my favorite bacterium. (That is saying something.) X. campestris is the source of xanthan gum which is in everything from face scrub to ice cream. It is especially important for gluten free baking because it holds everything together and also holds the air bubbles made by the leavening.

After 2 month of going gluten free, I finally made it to a Whole Foods where I got some xanthan gum. (I ordered some 1 month ago from Amazon, and I probably would have starved before it got here. It didn't get shipped until today!) I have been eating a lot of foods that do not require baking or leavening, but after 2 months, I was practically dreaming of anything starchy besides tapioca, Chex cereal, potatoes and rice. (I like them but they just don't quite make up for no wheat.) I made a pancake this morning with xanthan gum. It was my second attempt at a pancake. The first one held together because of the egg in the batter, but it was dense and heavy and not good. I added a little xanthan gum to a combination of potato starch, tapioca flour, and corn starch, baking powder, yogurt, water, egg and salt. Yum! Heaven in a skillet. Honestly, it was even lighter than those I used to make with wheat flour, and the flavor was nearly the same. I ate strawberry freezer jam on it and it was simply delicious.

Ahhhh.... X. campestris where would I be without you? (Still having ridiculous dreams about Midwestern agriculture probably). I hope your brief life in food production fermenters is so happy. You certainly deserve it for your excellent contributions to food web.

Wednesday, September 23, 2009

Working Late

I have heard a lot of evolutionary biologists say that religion is a crutch for those who are too emotionally weak to handle the realities of a harsh world. I am certain that is not the case for me because evolution is my crutch. My thesis advisor once told me he was amazed that when I was upset I could sit and unerringly set up dozens of experiments with tears streaming down my face. (I was always careful to keep the tears from falling into my experiments.) The reason I could do that is because lab work calms me down more quickly and certainly than anything else. Setting up experiments is a sort of meditation for me. It requires complete focus. It has a sort of rhythm to it, like breathing. It requires control of the body to stabilize hands, to left-handedly remove lids and pour liquids, and to maintain reasonably good posture for hours on end. The smells of the lab while not always pleasant, are at least familiar and comfortable and it is easy in that place to find the confidence and discipline necessary to work for hours at a time.

Currently, every cell of my body is aching to go to the hospital where my dad is recovering from a heart attack. But now isn't the right time. My dad is at the hospital and I couldn't see him much if I went anyway. They don't allow many visitors in his room. My mom is staying at the hospital with my dad as much as possible so I wouldn't get to see her much. He is recovering well and there are no farewells to be said at this point. It makes more sense for me to go in a week when my dad goes home and my mom goes back to work. They will need some help then.

Not to mention that I have work to do here...a journal article to review....a manuscript to submit...a collaborator who needs help preparing for an important talk.....bacteria to grow and then kill....students to advise and so on. But it is hard to really care about any of those things right now when all I want is to see for myself that my dad is okay.

Somehow in the midst of this, it is still easy to walk into the lab, and for the time I am in there, to fall completely into the comfortable routine of lab work.

Monday, September 14, 2009

MRSA on beaches. Ewwww.

The ICAAC meeting is going on in San Francisco right now. I went to the beta-lactamse dinner last night which Robert Bonomo always organizes wonderfully. It is always good to go and meet up with friends who share a love of bacteria and specifically beta-lactamases. It is fun when enough nerds gather that we can even have sub-groupings of nerds. The best part is that we can discuss really disgusting infections while eating Italian food and no one even thinks that it is strange or revolting.

One of the grossest findings presented at ICAAC so far is that MRSA is found on beaches. I think MRSA is probably everywhere. What this means for every day living: Disinfect every scrape or scratch or abrasion you get. MRSA would just love to infect your wound, even if it is really minor. It is still okay to go places and play and even get hurt a little bit. It is simply necessary to be a bit more attentive to even minor injuries.

Thursday, September 10, 2009

Polio Eradication Continues!


Hooray! The Taliban has stopped preventing polio vaccinations in Pakistan. Global polio eradication is becoming very close to reality and when it does it will be the second disease eradicated from human populations. The major roadblocks preventing complete eradication are uncooperative governments.

Here is a link to a good article.