I just found this article about scientific research on Lake Ellsworth in Antarctica. Really cool stuff (no pun intended). Contrary to popular opinion, the region is not dead or devoid of life. There is a lot of life beyond what you can see. And while the microbial life happens very slowly there, it still happens. The microbes just have to deal with some extreme stress issues (and bacteria, in general, are very good at doing that). Extreme cold, UV exposure, drying.
Many years ago I met a microbiologist by the name of Robie Vestal who spent some time there doing some microbiology research.
I’ve always loved the idea of the ecosystem he described living a few millimeters WITHIN rocks. Yup—actually inside sandstone. I couldn’t find a picture of the actual Antarctic rocks, but go to this site, scroll down to the third picture, and look at a similar rock found in Yellowstone National Park to get an idea of what such a layer would look like. When they cut into the rocks, there was this thin layer 1 – 10 millimeters inside it. When they looked at it in detail, they found a group of microorganisms inside there. It was a lichen—similar to those that you find on tree bark, or on rock surfaces, but this one lives inside Antarctic rocks.
Lichens are interesting because they are an example of mutualism in action. A lichen is 2 different organisms (sometimes more) living together in a mutually beneficial fashion. One component is a fungus, and the other is an alga or a bacterium. The alga or the bacterium within the lichen is photosynthetic, which means it gathers its energy from sunlight (just like green plants), and provides the primary energy in the system. The fungus lives off of the chemicals (metabolic products) made by the bacterium or alga. The fungus can soak up water better, providing that for the photosynthetic part of the lichen. The bacteria or algae cells live intertwined within the hyphae (hair like structures) made by the fungi.
The lichen takes up residence inside the Antarctic rocks probably because it’s just a little warmer and less dry than living on the surface of the rock. It grows VERY slowly, but it’s there and metabolically active.
NASA is very interested in biological research in Antarctica because it’s one of the few places on Earth that may hold relevance for finding life off of Earth. This is a field of research known as Exobiology. The idea is that if we can understand how microbes withstand extreme environments on our own world, then we may understand what sites to look at on other planets for life or the remnants of extinct life. And the water in the underground Lake Ellsworth is certainly an example of extreme stress. Futhermore, by studying life in extreme situations, we may get a better understanding of how life survived on the early Earth, when the conditions weren't as favorable as they are today.
Tuesday, January 29, 2008
Monday, January 28, 2008
Genes, DNA, Chromosomes, Genome: The Heredity Bunch!
So, what’s a gene? Inside each of our cells (except red blood cells, which is another story), we have deoxyribonucleic acid (DNA) molecules. Genes are pieces of DNA that serve as the units of heredity. In cells the DNA is organized into chromosomes, and the entire chromosome complement of a cell is called its genome. Genes contain the code for proteins.
In fact, every living cell, be it a human cell, animal cell, plant cell, yeast cell, fungus cell, protozoan cell, or a bacterial cell has DNA in it. It’s the blueprint of life. It’s what guides every aspect of life development. Our DNA is the guidebook that told our cells to develop as human. My dog’s DNA has many similarities to mine, but enough differences so that she’s not human, she’s a dog (although sometimes it’s uncanny how “human” she can act—also, another story).
DNA guides the chemistry of life. Each gene codes for something—mostly proteins. Another molecule, RNA (ribonucleic acid) is the immediate result of the biochemical reading of DNA. RNA is the carrier of the message to the workhorse of the cell, the ribosome. The ribosome reads the RNA, and a protein is made from the messenger RNA (mRNA).
It’s those proteins that do the work that keeps everything going. They keep the cells burning energy, determine your eye color, determine your development and growth, determine if your earlobes are attached or not, and build the machinery that is your body. All things mundane and fabulous.
DNA is an organic molecule (there’s that word again), meaning that the molecule is constructed on a backbone of Carbon molecules. The molecule is a very long chain that consists of 2 strands organized into a double helix structure. The two strands are bound together along their length. The long DNA chains are made up of nucleotides along a backbone made up of sugars (dexoyribose) and phosphate molecules. Attached to these sugar molecules are organic bases. There are 4 bases in DNA: Adenine (A), Guanine (G), Cytosine (T), and Thymine (T). See the pictures at the top for cartoons of DNA structure and the chemical structure of a C-T base pair.
RNA is a single helix made up of nucleotides along a backbone made up of the sugar ribose with phosphate molecules. Three of the bases in RNA are the same as those in DNA: Adenine (A), Guanine (G), and Cytosine (C); however, there is no thymine in RNA. It is replaced with another base named Uracil (U).
One analogy for DNA is that it’s an alphabet. However, this alphabet only has 4 letters: AGCT. All the variability in life on Earth is derived from different combinations of AGCT.
The two helices of the DNA molecule are connected to each other through bonds between the base molecules on each strand. However, A’s only pair up with T’s, and C’s only pair up with G’s. In that way, the 2 strands complement each other.
Length in DNA is measured in bases. A gene can be hundreds to thousands (kilobases) of bases long, so those 4 bases can combine into countless unique combinations. Hence the genetic variability of life on Earth. Each cell that contains a genome is like a hard drive on a computer. All the information necessary to run all of the functions is contained there. That’s a lot of information! So, there’s a lot of DNA in each cell. How much? If the contents of one human cell’s genome was arranged in a straight line, it would be over 6 feet long! And there are anywhere between 10 and 100 trillion cells in our bodies! (60 – 600 trillion feet of DNA/person! -- 113 billion miles or 182 billion kilometers!)
DNA is the molecule (and an elegant one at that). Genes are pieces of DNA that code for proteins (mostly). The genes and DNA are organized into chromosomes (humans have 23 pairs of chromosomes). All of the genetic information in the nucleus is the genome. So, when they say that they’ve sequenced the human genome, that means they’ve determined the DNA sequence (the combination of AGCT) for each chromosome. In a human male, that’s 3 billion DNA nucleotide pairs!
In fact, every living cell, be it a human cell, animal cell, plant cell, yeast cell, fungus cell, protozoan cell, or a bacterial cell has DNA in it. It’s the blueprint of life. It’s what guides every aspect of life development. Our DNA is the guidebook that told our cells to develop as human. My dog’s DNA has many similarities to mine, but enough differences so that she’s not human, she’s a dog (although sometimes it’s uncanny how “human” she can act—also, another story).
DNA guides the chemistry of life. Each gene codes for something—mostly proteins. Another molecule, RNA (ribonucleic acid) is the immediate result of the biochemical reading of DNA. RNA is the carrier of the message to the workhorse of the cell, the ribosome. The ribosome reads the RNA, and a protein is made from the messenger RNA (mRNA).
It’s those proteins that do the work that keeps everything going. They keep the cells burning energy, determine your eye color, determine your development and growth, determine if your earlobes are attached or not, and build the machinery that is your body. All things mundane and fabulous.
DNA is an organic molecule (there’s that word again), meaning that the molecule is constructed on a backbone of Carbon molecules. The molecule is a very long chain that consists of 2 strands organized into a double helix structure. The two strands are bound together along their length. The long DNA chains are made up of nucleotides along a backbone made up of sugars (dexoyribose) and phosphate molecules. Attached to these sugar molecules are organic bases. There are 4 bases in DNA: Adenine (A), Guanine (G), Cytosine (T), and Thymine (T). See the pictures at the top for cartoons of DNA structure and the chemical structure of a C-T base pair.
RNA is a single helix made up of nucleotides along a backbone made up of the sugar ribose with phosphate molecules. Three of the bases in RNA are the same as those in DNA: Adenine (A), Guanine (G), and Cytosine (C); however, there is no thymine in RNA. It is replaced with another base named Uracil (U).
One analogy for DNA is that it’s an alphabet. However, this alphabet only has 4 letters: AGCT. All the variability in life on Earth is derived from different combinations of AGCT.
The two helices of the DNA molecule are connected to each other through bonds between the base molecules on each strand. However, A’s only pair up with T’s, and C’s only pair up with G’s. In that way, the 2 strands complement each other.
Length in DNA is measured in bases. A gene can be hundreds to thousands (kilobases) of bases long, so those 4 bases can combine into countless unique combinations. Hence the genetic variability of life on Earth. Each cell that contains a genome is like a hard drive on a computer. All the information necessary to run all of the functions is contained there. That’s a lot of information! So, there’s a lot of DNA in each cell. How much? If the contents of one human cell’s genome was arranged in a straight line, it would be over 6 feet long! And there are anywhere between 10 and 100 trillion cells in our bodies! (60 – 600 trillion feet of DNA/person! -- 113 billion miles or 182 billion kilometers!)
DNA is the molecule (and an elegant one at that). Genes are pieces of DNA that code for proteins (mostly). The genes and DNA are organized into chromosomes (humans have 23 pairs of chromosomes). All of the genetic information in the nucleus is the genome. So, when they say that they’ve sequenced the human genome, that means they’ve determined the DNA sequence (the combination of AGCT) for each chromosome. In a human male, that’s 3 billion DNA nucleotide pairs!
Friday, January 11, 2008
I'm a Cloner! Wouldn't you like to be a cloner too?
It’s funny how words take on meanings in the cultural consciousness that are different from what they actually mean. I can think of several examples of words used in various fields of science that have taken on new or slightly different meanings when used in a broad context, such as in the public as a whole. One that comes to mind is the word clone (or cloning).
I am a cloner. I have cloned things. Many things. There. I’ve said it. And I’m proud of it.
No, I have not cloned a sheep, a cat, a cow, or even a horse. I have cloned genes.
The word “clone” can be a noun or a verb. As a verb, it is the act of making a copy of something. The noun “clone” means to be genetically identical to something else. So, the genes I have cloned are clones of the genes they were originally cloned from.
Seriously though, it just means duplicates or copies. Exact copies. There are other meanings that have made their way into common speech (PC computers used to be called IBM clones, for example).
Many scientists clone. Very few clone animals. Those that do clone, clone genes.
And cloning genes, doing molecular biology, while it can be frustrating is actually kind of fun. It’s like doing a logic puzzle. DNA, while a complex molecule, is quite elegant. You can make maps of DNA molecules. At the top of this entry is a map of a plasmid (a small, circular piece of DNA--this one is 2686 base pairs long). We use maps often. And on these maps are markers—road signs in a way. These are called restriction sites.
I am a cloner. I have cloned things. Many things. There. I’ve said it. And I’m proud of it.
No, I have not cloned a sheep, a cat, a cow, or even a horse. I have cloned genes.
The word “clone” can be a noun or a verb. As a verb, it is the act of making a copy of something. The noun “clone” means to be genetically identical to something else. So, the genes I have cloned are clones of the genes they were originally cloned from.
Seriously though, it just means duplicates or copies. Exact copies. There are other meanings that have made their way into common speech (PC computers used to be called IBM clones, for example).
Many scientists clone. Very few clone animals. Those that do clone, clone genes.
And cloning genes, doing molecular biology, while it can be frustrating is actually kind of fun. It’s like doing a logic puzzle. DNA, while a complex molecule, is quite elegant. You can make maps of DNA molecules. At the top of this entry is a map of a plasmid (a small, circular piece of DNA--this one is 2686 base pairs long). We use maps often. And on these maps are markers—road signs in a way. These are called restriction sites.
Restriction enzymes (the real term is restriction endonuclease) cut DNA molecules at very specific sequences in the DNA. So, you can use these restriction enzymes to cut the DNA in a predictable manner, and take a piece of DNA from one strand by cutting it with a particular restriction enzyme and insert it into another strand of DNA that has been cut with that same restriction enzyme. The ends will be compatible. In its most basic form, this is cloning.
In the plasmid map at the top, the restriction sites are the ones labeled all along the outside of the circle. They have names like SspI, NdeI, BsaXI, etc. Each of the enzymes listed have a different DNA recognition sequence (a specific sequence of the ACGT molecules that make up DNA).
And when you have a bunch of pieces of DNA you have to put together in a map—it really is a logic puzzle.
If you like crossword puzzles, you may have an aptitude for molecular biology.
And when you have a bunch of pieces of DNA you have to put together in a map—it really is a logic puzzle.
If you like crossword puzzles, you may have an aptitude for molecular biology.
Note: It was far too long and confusing to explain cloning, DNA structure, and genes all in one blog entry. In the next couple of days I'll post a basic explanation of genes, DNA, and chromosomes.
Friday, January 4, 2008
Musings on Science and Women and Science and Kids
I heard a statistic while listening to NPR recently that girls start to ignore or doubt their aptitude in math before they’re 10 years old. I read the statistics, and I see the op-ed’s in newspapers about how girls are not going into math and science careers. And while I don’t doubt that it is at least partially true, I have to say that in my own experience, I know a lot of women who have chosen math and science careers.
Maybe that’s because I’m in the biological sciences, which does seem to attract more women than, for example, physical sciences or chemistry. But when I was in graduate school, I would say that the majority of my colleagues there were women. In fact, at one point, the lab I was training in had about 6 or 7 females and only 1 man.
After I got my Ph.D. and went on to do post-doctoral training (as is usual for bio-science doctorates), I would say that the ratio of men:women was about 1:1. The generation ahead of me, however, was not so equitable.
Most of my professors were men. Many of them were quite enlightened about having women in their lab. I would have to say that I’ve been really lucky. I can only really think of one case where I felt that I was treated unfairly in a situation, and that it possibly may have been because I was a woman. While a big deal for me at the time, I did make it through the task just fine, and I haven’t really noticed anything like that since. I have been lucky to have wonderful mentors, and to live in a generation that promoted women’s ambitions.
I have heard horror stories from the women who paved the way in the generation before. The stories they told were of male professors who would pass them over in favor of male students for spots in labs because they figured the women weren’t actually serious about their careers. If you’re in graduate school, you’re serious about your field. There were male professors who failed to help women graduate students when it came time to graduate and move on to post-doctoral work, simply because they couldn’t imagine why a woman would want to do it. Well, it’s what you do after you get the degree—move on to the next step in your training. Then there was the real need for these women to not only do well when they finally got faculty positions (which was incredibly difficult for them in the 1960’s), but to excel so much more than their male colleagues just to show that they should be taken seriously.
I am grateful for the women who blazed the trail before me. I think their hard work was reflected in the number of wonderful women scientists I’ve encountered as colleagues along my way.
So, when I hear about girls losing interest in math and science at young ages, it distresses me. I recognize that everyone has different interests, and the technical fields are not for everyone. I’m thinking of people now who do have the aptitude, but lose interest because of some sort of outside pressure. Where and when does the shift in a girl’s mind happen when she thinks she can’t handle math and science anymore?
Here’s a Washington Post article that suggests it’s social pressure, and that it can be overcome. I actually know some wonderful elementary and middle school math and science teachers who are doing great jobs with their kids. I’ve visited a couple of their classrooms and have been impressed with their dedication and enthusiasm. I judge regularly in local science fairs, and see some great questions and great method being used by kids as young as 7th grade.
Here’s the interesting thing though—while the most detailed studies in these science fairs are done by kids in 11th and 12th grades, the more fun projects, and the greatest number of projects, are being done by kids in 7th and 8th grades. It’s a blast to read and judge the 7th and 8th grade projects! I actually learn a lot from them (and get ashamed by the amount of stuff I’ve forgotten over the years).
So, I ask, does science stop being fun after that? Puberty hits with a vengeance, kids start thinking about other things, social pressure.
I may be a bit rambling in this post, but I’m kind of thinking out loud. Any ideas?
Maybe that’s because I’m in the biological sciences, which does seem to attract more women than, for example, physical sciences or chemistry. But when I was in graduate school, I would say that the majority of my colleagues there were women. In fact, at one point, the lab I was training in had about 6 or 7 females and only 1 man.
After I got my Ph.D. and went on to do post-doctoral training (as is usual for bio-science doctorates), I would say that the ratio of men:women was about 1:1. The generation ahead of me, however, was not so equitable.
Most of my professors were men. Many of them were quite enlightened about having women in their lab. I would have to say that I’ve been really lucky. I can only really think of one case where I felt that I was treated unfairly in a situation, and that it possibly may have been because I was a woman. While a big deal for me at the time, I did make it through the task just fine, and I haven’t really noticed anything like that since. I have been lucky to have wonderful mentors, and to live in a generation that promoted women’s ambitions.
I have heard horror stories from the women who paved the way in the generation before. The stories they told were of male professors who would pass them over in favor of male students for spots in labs because they figured the women weren’t actually serious about their careers. If you’re in graduate school, you’re serious about your field. There were male professors who failed to help women graduate students when it came time to graduate and move on to post-doctoral work, simply because they couldn’t imagine why a woman would want to do it. Well, it’s what you do after you get the degree—move on to the next step in your training. Then there was the real need for these women to not only do well when they finally got faculty positions (which was incredibly difficult for them in the 1960’s), but to excel so much more than their male colleagues just to show that they should be taken seriously.
I am grateful for the women who blazed the trail before me. I think their hard work was reflected in the number of wonderful women scientists I’ve encountered as colleagues along my way.
So, when I hear about girls losing interest in math and science at young ages, it distresses me. I recognize that everyone has different interests, and the technical fields are not for everyone. I’m thinking of people now who do have the aptitude, but lose interest because of some sort of outside pressure. Where and when does the shift in a girl’s mind happen when she thinks she can’t handle math and science anymore?
Here’s a Washington Post article that suggests it’s social pressure, and that it can be overcome. I actually know some wonderful elementary and middle school math and science teachers who are doing great jobs with their kids. I’ve visited a couple of their classrooms and have been impressed with their dedication and enthusiasm. I judge regularly in local science fairs, and see some great questions and great method being used by kids as young as 7th grade.
Here’s the interesting thing though—while the most detailed studies in these science fairs are done by kids in 11th and 12th grades, the more fun projects, and the greatest number of projects, are being done by kids in 7th and 8th grades. It’s a blast to read and judge the 7th and 8th grade projects! I actually learn a lot from them (and get ashamed by the amount of stuff I’ve forgotten over the years).
So, I ask, does science stop being fun after that? Puberty hits with a vengeance, kids start thinking about other things, social pressure.
I may be a bit rambling in this post, but I’m kind of thinking out loud. Any ideas?
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