I am leaving academia. And I'm not bitter. I only say that because I get the feeling many of the people leaving academia are leaving because they're bitter they haven't been offered the dream faculty position they've been told they deserve.
I am leaving to get back to nature. I started doing science as a way to express my love of nature, and to follow my curiosity of how organisms evolve and interact to create the lovely biodiversity we see every time we walk outside. The only problem is, the more I advance within academia, the less I am able to go for those walks outside to appreciate nature. I am usually up (and in the winter, at work) before the sun rises, work in an artificially lit environment all day either staring at a computer screen or moving infinitely small volumes of liquid from one container to another, and then leave after ~10+ hours of this for some hope of a few hours down time (which can include lots of work-related reading) before starting it all again the next day.
Don't get me wrong, I love research. I love learning new things and living on the edge of human knowledge. But the cost is that I rarely get to interact with nature anymore, the very love that drove me to this crazy lifestyle. I miss her. My heart aches for a chance to be with her. It is worth the feelings of failure, for that is how most people look at the lost academic.
What am I doing next? That is a topic for tomorrow...
January 25, 2012
July 13, 2011
Genetic engineering: good or bad?
As a scientist I've never really understood the objections to the genetic engineering of organisms. We do it with bacteria all the time in the laboratory so that we can use them to study the biology of many different organisms including plants, animals, etc. Furthermore, genetic manipulation of bacteria is widely used in industry for the production of drugs and other compounds such as enzymes, vitamins, etc. It is cheaper and more efficient to use the bacteria to do the work, rather than extracting (or synthesizing) these molecules from their native hosts. So why are some people so upset about the modification of genes? I always thought that they just didn't understand science. I always wondered why they cared so much about GM food but not about the GM drug prescriptions they were filling. The hypocrisy was irritating to me. I finally hit the tipping point when I read in a rural newsletter about the "dangers" of GM crops. I was fed up and wanted to understand the opposition, so I bought a few books. One of these books was obviously anti-GM, the other was very much pro-GM, and the third book was sort of a mediator, providing evidence for the good and the bad.
After reading these three books, I've completely changed my mind about the usefulness of genetic modification. I am still not opposed to genetic manipulation in principle, but am mostly opposed to it in practice. I will go into more detail in future blog posts.
One of the reasons I am most interested in this debate is that I am worried about the future of microbial ecology research and the ways in which this could affect treatments of diseases. I envision a day where people are given a bacterial species as medicine to help cure intestinal problems (e.g., Crohn's disease). In fact this is already happening with probiotic supplements, and the amount of research going into other microbial treatments is staggering. But the delivery of these treatments needs to be done in a way that helps educate the public rather than scare them, as has been done with the GM debacle. Hopefully I can help out with this public education endeavor. Any suggestions?
After reading these three books, I've completely changed my mind about the usefulness of genetic modification. I am still not opposed to genetic manipulation in principle, but am mostly opposed to it in practice. I will go into more detail in future blog posts.
One of the reasons I am most interested in this debate is that I am worried about the future of microbial ecology research and the ways in which this could affect treatments of diseases. I envision a day where people are given a bacterial species as medicine to help cure intestinal problems (e.g., Crohn's disease). In fact this is already happening with probiotic supplements, and the amount of research going into other microbial treatments is staggering. But the delivery of these treatments needs to be done in a way that helps educate the public rather than scare them, as has been done with the GM debacle. Hopefully I can help out with this public education endeavor. Any suggestions?
June 5, 2011
Microbes in saliva
I did a small experiment as part of my larger research project. I wanted to find out how many different bacterial species were living in my saliva. In our lab we look at the bacteria in human samples all the time, so I decided to include my own saliva in one of these test runs. One morning I spat in a tube several times, until I had spat around 5 milliliters, and then capped it and took it to work. I spat before I had brushed my teeth, hoping to get the maximum number of bacterial species. At work I extracted DNA from this saliva sample and then ran it through our handy dandy DNA sequencer to see what was in there. (Identifying bacteria by sequencing DNA is very common these days. I'll write more about this later.) I also used some of this DNA to test some purification methods our laboratory is trying to develop, so it wasn't a completely selfish exercise.
Lo and behold, when the results were in, I was surprised to find out how much diversity was present in my mouth. I am still analyzing the data, and will write more about it later, but I will tell you that there were probably hundreds of bacterial species present in my saliva sample. Scientists have known for a long time that bacteria are abundant in saliva. After all, bacterial biofilms are what constitute plaque. But I was very surprised to learn that the number of species was so high. Now there are some difficulties defining what a species is in bacteria (I'll write more about this later too), but suffice it to say, hundreds of bacteria are calling my mouth home.
Lo and behold, when the results were in, I was surprised to find out how much diversity was present in my mouth. I am still analyzing the data, and will write more about it later, but I will tell you that there were probably hundreds of bacterial species present in my saliva sample. Scientists have known for a long time that bacteria are abundant in saliva. After all, bacterial biofilms are what constitute plaque. But I was very surprised to learn that the number of species was so high. Now there are some difficulties defining what a species is in bacteria (I'll write more about this later too), but suffice it to say, hundreds of bacteria are calling my mouth home.
May 9, 2011
What is the natural function of antibiotics?
This is a burning question on my mind lately. As a microbiologist I've been taught that antibiotics exist for the medical profession to help treat infectious diseases, and oh yeah, for scientists to use in their experiments (for a plethora of reasons). Obviously antibiotic production didn't evolve for humans to take advantage of it....so why did it evolve?
Important things to keep in mind:
1. Antibiotics as they are used in medicine, agriculture, and aquaculture are at concentrations orders of magnitude higher than what would be produced naturally by the organisms in which their production evolved.
2. Bacteria (and other microbes) are known to exist in nature very differently than they do in the laboratory.
Bottom line:
The way(s) antibiotics affect bacteria in the lab may not be the way they affect bacteria in nature. More on this later...
Important things to keep in mind:
1. Antibiotics as they are used in medicine, agriculture, and aquaculture are at concentrations orders of magnitude higher than what would be produced naturally by the organisms in which their production evolved.
2. Bacteria (and other microbes) are known to exist in nature very differently than they do in the laboratory.
Bottom line:
The way(s) antibiotics affect bacteria in the lab may not be the way they affect bacteria in nature. More on this later...
May 3, 2011
Jiffy pot surprise
As I venture into my new role as amateur gardener, I am slowly realizing I have lots to learn. I was really pumped to sow some seeds indoors then transplant them when it gets warmer. So I collected some Jiffy pots from my pseudo-mom and started sowing. About one week later I noticed sprouts! Seedlings abound! But what I hadn't anticipated were the fungal cells multiplying at the same time. Now there is a furry white film around the top of my Jiffy pots. Luckily the fungal hyphae didn't extend onto the plant sprouts. I distanced the pots from one another so they could dry out better. I also turned on a space heater and sprayed them with 0.3% hydrogen peroxide. Hopefully it works!
Fungal cells or spores must have been hiding out in the Jiffy pots, waiting for moisture and nutrients. When I added the soil and water, covered the pots to keep moisture in, and left them in indirect sunlight, the fungi must have found ideal conditions for multiplication. Extensions of single cells in to mycelium networks now made a visible mark on my pots. I wonder how long they had been in the pots. Since manufacture? Or perhaps they were stored in pseudo-mom's greenhouse for too long, in an opened package nonetheless. I will never know I guess. I only wish I had microscope at home to take a closer look!
Fungal cells or spores must have been hiding out in the Jiffy pots, waiting for moisture and nutrients. When I added the soil and water, covered the pots to keep moisture in, and left them in indirect sunlight, the fungi must have found ideal conditions for multiplication. Extensions of single cells in to mycelium networks now made a visible mark on my pots. I wonder how long they had been in the pots. Since manufacture? Or perhaps they were stored in pseudo-mom's greenhouse for too long, in an opened package nonetheless. I will never know I guess. I only wish I had microscope at home to take a closer look!
May 1, 2011
Ewwww!
The often cited statistic is this: only one in ten cells of the human body is human. What are the other nine? Microbial cells. Cells from really small mites and worms, but also cells from bacteria and single-celled eukaryotes. Huh? Euk, what?
Biologists like to give fancy names to not-so-fancy differences. Of all the cells in the world, they can be divided in to two types: those with a nucleus (eukaryote) and those without a nucleus (a prokaryote). We are eukaryotes made of many cells, and can be seen without a microscope. So we're macroscopic multicellular eukaryotes. But there are also really small eukaryotes that one would need a microscope to see. We call those microbial eukaryotes. These include a lot of fungi (which can become macroscopic when cells join forces to make fruiting structures like mushrooms) and scary things like plasmodium, the cause of malaria.
Prokaryotes are all single-celled organisms, which means that they exist as individual cells. Bacteria are prokaryotes, and so are a related group of organisms called the Archaea. But back to the human body.
Only one in ten cells is human? Why don't we look like a gimush of bacteria and other microbes? Well, human cells are about 10 times bigger than bacterial cells, so we only see the human composite. But if we had microscopic vision, we'd see a whole different picture.
This is precisely what a lot of scientists are doing right now, not with microscopes, but with DNA sequencers. They're taking samples of humans and sequencing DNA to identify and classify the bacteria and other microbes present, which collectively are referred to as the 'Human Microbiome'. We want to determine the microbiome for people with different diseases (Crohn's disease, IBS, obesity, etc.) and compare them to the microbiomes of people without these diseases. These comparisons might tell us how microbiomes differ in diseased individuals so that one day we may be able to treat them by altering the microbiome ecosystem. For example, we could provide them with a beneficial bacterial species that kills a harmful bacterial species.
How do you feel about swallowing bacteria to treat disease?
Biologists like to give fancy names to not-so-fancy differences. Of all the cells in the world, they can be divided in to two types: those with a nucleus (eukaryote) and those without a nucleus (a prokaryote). We are eukaryotes made of many cells, and can be seen without a microscope. So we're macroscopic multicellular eukaryotes. But there are also really small eukaryotes that one would need a microscope to see. We call those microbial eukaryotes. These include a lot of fungi (which can become macroscopic when cells join forces to make fruiting structures like mushrooms) and scary things like plasmodium, the cause of malaria.
Prokaryotes are all single-celled organisms, which means that they exist as individual cells. Bacteria are prokaryotes, and so are a related group of organisms called the Archaea. But back to the human body.
Only one in ten cells is human? Why don't we look like a gimush of bacteria and other microbes? Well, human cells are about 10 times bigger than bacterial cells, so we only see the human composite. But if we had microscopic vision, we'd see a whole different picture.
This is precisely what a lot of scientists are doing right now, not with microscopes, but with DNA sequencers. They're taking samples of humans and sequencing DNA to identify and classify the bacteria and other microbes present, which collectively are referred to as the 'Human Microbiome'. We want to determine the microbiome for people with different diseases (Crohn's disease, IBS, obesity, etc.) and compare them to the microbiomes of people without these diseases. These comparisons might tell us how microbiomes differ in diseased individuals so that one day we may be able to treat them by altering the microbiome ecosystem. For example, we could provide them with a beneficial bacterial species that kills a harmful bacterial species.
How do you feel about swallowing bacteria to treat disease?
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