Tuesday, September 25, 2007

Microbios Gigantes!

As a follow up to the previous post... If you have been left so fascinated by microbes that you wish you could just hug them, here's your chance: http://www.giantmicrobes.com/


A while ago I gave Salmonella and Lyme Disease to my friend Michelle, and Girardia and an Ulcer to my friend Mo. :-)

And you thought you were alone...

Did you know that we have 10X more bacteria in our gut than cells in our body? That makes me wonder if we are who we think we are. It may be time to rethink the species concept...

Advances in technology usually open doors for the exploration of new and exciting questions and this is certainly the case with advances in genome exploration technology. Thanks to shot-gun sequencing and microarray techniques it is now possible to study the symbiotic interaction between us "higher organisms" and our more numerous cohabitants, the tiny microbes.

Metagenomics, a new and exciting field of research (with an equally catchy name), attempts to study communities of microbes directly in their natural environments (e.g. your gut, your mouth, a patch of dirt, the ocean, etc.). By using modern genome sequencing techniques, metagenomics bypasses the need for lab cultivation of individual species. This is a huge step forward because it is estimated that we have only been able to isolate and culture just 1% of all microorganisms in nature. Metagenomics, thus, offers the chance to identify a wider array of microorganisms than previously possible. This new technology also allows the study of the little buggers in their natural setting (e.g. the complex crevices of your nose) as opposed to the artificial conditions of a petri dish.

This field of study offers so much promise that the National Institutes of Health (NIH), the leading biomedical research funding agency in the U.S., has recently announced a new initiative to probe the human microbiome. This ambitious enterprise, which is part of the NIH's Roadmap for Medical Research, will focus on characterizing the populations that our bodies play host to and their role in health and disease.

But microbial populations are not just important for health. Microbe communities are also responsible for maintaining atmospheric balances of CO2, for supporting the health of crops (and in some cases causing their disease), and many types microorganisms produce potential alternative energy sources such as hydrogen, butanol, and methane. Clearly, (and whether we like it or not) these guys make life on this planet what it is and we have only yet begun to understand how it is they do it.

Interested in learning more? The National Academies has recently published a beautiful educational brochure on metagenomics and the importance of studying microbial communities. This brochure is freely downloadable here, where you can also request hardcopies for educational purposes.

Here are also some recent metagenomics publications:

  • Metagenomics of the deep mediterranean, a warm bathypelagic habitat. PLoS ONE
  • The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biology
  • Metabolomics of a superorganism. J Nutrition
  • An obesity-associated gut microbiome with increased capacity for energy harvest. Nature
  • Metagenomic analysis of the human distal gut microbiome. Science

Monday, September 24, 2007

Dust in the wind?

Not too long ago, I got into an interesting conversation about science, consciousness, and spirituality. While, I consider myself an atheist because I do not believe in the existence of a god or a higher power, the other person maintained that no one is an atheist unless they are truly a-spiritual, that is, do not believe in any transcendence for the human experience. I interpreted this as more of a question of semantics, but our conversation got me thinking about what I really believe in regarding our place in this world and the meaning of our lives. So, dear imaginary (nonexistent) reader, brace yourself because we will attempt to swim out to the deep end of the pool and explore the outer limits of science, religion, and my humble opinion about the meaning of existence (you may want to grab a floatie).

I have considered myself an atheist since the age of fifteen or sixteen... I'm not really sure how the realization came upon me. I had been raised catholic, though admittedly not very strongly. My father went to church maybe twice or three times a month and considered himself religious but my mother didn't want to have anything to do with the church--she has always been a bit of an activist for the separation of church and state. I had gone through catechism and first communion and remember being inspired at a young age by the stories of Jesus and his kindness and love for his fellow humans. I did not however enjoy mass. Perhaps it was that the priests of my church were not themselves particularly inspiring. They were strict and dogmatic and I did not feel from them the love and kindness that had initially attracted me to religion. Starting in my teens, I began to have increasing doubts and a creeping suspicion that our lives were made of flesh and bone and that everything stopped after we died. I don't know how these thoughts came about. At that age I enjoyed science but I still had not found in it a vocation. I just had a gut feeling, and to be honest it wasn't a very good feeling at all. At night, I would have to push away thoughts about death because the anxiety it produced would not let me fall asleep. Even today I still have to make a conscious effort to withdraw my mind when these considerations start creeping in. I am afraid of death and I have no qualm in admitting it.

So my disbelief in God at a young age came from a "gut feeling", not from a positivist belief that the scientific method is the sole determination of what is real and what is not real. I am OK with this, and on some level I believe that this is the way it should be--personal religious opinions, whatever they may be, separate from science.

Religion and spirituality are not supposed to be held to account with the laws of physics. Because of mysticism, they have an inherent get-out-of-jail free card. For example, Christianity has what are termed "mysteries", i.e. supernatural truths that are unattainable to humans through reason. This is an intrinsic part of faith and it makes it futile to try to apply logic or empiricism to religion (there is no arguing with something that does not accept rational argument).

Also, and at the risk of getting flack from hard-core science champions, it may well be that science will only take us so far in our understanding of the world, our brains creating some sort of biological limit for what may be probed and understood. Although so far there has been no indication that this might be the case, there is the possibility that there might be a reality beyond what we are physically able to discern.

And in terms of the regrettable debate between faith and science, it is definitely best to keep the two separate. Everyone has the right to believe what they want to believe (especially the pastafarians). And even the most devout scientist may still believe in a higher power. My point is that our choice of religious or spiritual belief is valid and is outside of the realm of science even if it is within what some would consider an absolute physical reality...

An absolute physical reality, yet spiritual beliefs? Getting confused? Well so am I, but here's where the thicket of the jungle starts. How can one believe in spirituality if one believes that it is all in one's head so to speak? In other words, what happens when you believe that the experience of existence is nothing more than the product of that wonderful biological fortuity, the brain? What does this mean for spirituality?

I am still mulling these things over and it may take me a while to come up with a rational thesis (at this point you could say that I have a "gut feeling"), so I'll leave these questions open for now....

Sunday, September 23, 2007

The most enjoyable depressing book you'll ever read

The Grass is Singing, by Doris Lessing

Well, I guess I wouldn't really say that I enjoyed this book--how can anyone really enjoy the telling of the maddeningly slow yet unmitigated disintegration of a woman and her psyche--but it was nonetheless an engrossing read.

The main character, Mary Turner, is an odd bird. The first half of her life, is an unremarkable, daze. She lives life content and complacent with her lack of goals and meaningful personal relations. The woman is almost pathological in her tendency not to leave a trace in the world, or rather, in not letting the world leave a trace in her. She never falls in love or allows anyone else to fall in love with her and she never fosters any personal desires or dreams. She lives a boring life of consistency. The author attempts to give us a psychological explanation of why she is this way--something to do with her suffering mother and her drunkard father--but it is not very convincing (at least to me). What is convincing is the sense that Mary is not a likable woman and that perhaps she is not in full possession of a sound resilient character.

Mary's reasons for marrying Dick are equally strange. She does it because she suddenly realizes that as a single woman, she is the object of people's pity. She thus moves out into the African bush, where Dick has a shabby house on the skirts of a shabby farm. From this point on the mood turns from drab to dark. Little by little, the sun, the poverty, the loneliness, the unyielding heat, and her hatred for "the natives", begin whittling Mary's character and sanity down until there is nothing left but a shriveled-up carcass of a woman and a human being. Ironically, it is a hateful act that Mary commits toward a black farm laborer that makes her start seeing him for the very first time. In her broken down state, this new vision becomes a sick obsession, and it finally explodes with tragic consequences.

Mary's life, we know, is also a parable for racism, colonialism, and white supremacy in Africa and the destructive effect they had on the individuals and its society.

So, yeah, a real pick-me-upper... But what was weird was that, while I could not identify with the characters and, in fact, rejected their weaknesses and faults, I could not put the book down. I tortured myself metro ride after metro ride with this story of a crazy white lady in crazy-white South Africa. I think this was due to Doris Lessing wonderful writing. The author creates a hypnotic psychological vortex in the hot and arid lands of the African bush and she is not afraid to take it to its ultimate conclusion.

See my Goodreads page here.