Tuesday, October 31, 2006
Hubble Makes Me Happy
YAY! Hubble will stay up to roughly 2013, around the same time that its replacement will be launched. Happy dance!
Saturday, October 21, 2006
Demon-Haunted Hotels
Just a quick note to point you to my new project, Demon-Haunted Hotels . Help us light the candle!
Monday, October 16, 2006
Bright White Disc
Just a quick note to make sure everyone sees today's APOD. Look closely. That picture has everything:
* A new discovery: from that angle, Cassini was able to show us new rings that we'd never been able to see before.
* The wonders of modern technology: We launched Cassini on October 15, 1997. Since then it has traveled the millions of miles to Saturn (first whipping around the Sun and passing just near enough to Venus, Earth, and Jupiter to get gravity kicks to send it out to Saturn), orbited Saturn itself several times, helped us discover 2 moons of Saturn (among many other scientific achievements, including a confirmation of Einstein's general relativity just for kicks), and, of course, lined itself up nicely to place Saturn between itself and the Sun and snap that wonderful picture.
* Humility: In case you don't read the description provided by NASA, that spec of dust on the left side of the photo, just above and outside the brightest rings, is the first planet discovered by man, although it took us thousands of years from the time we first named it until the time we realized it was anything like the other planets. That spec of dust, of course, is the pale blue dot we call home.
For those who won't follow that last link, you owe it to yourself to read what Sagan said about that pale blue dot, even without a giant planet in the foreground to make it seems even smaller:
* A new discovery: from that angle, Cassini was able to show us new rings that we'd never been able to see before.
* The wonders of modern technology: We launched Cassini on October 15, 1997. Since then it has traveled the millions of miles to Saturn (first whipping around the Sun and passing just near enough to Venus, Earth, and Jupiter to get gravity kicks to send it out to Saturn), orbited Saturn itself several times, helped us discover 2 moons of Saturn (among many other scientific achievements, including a confirmation of Einstein's general relativity just for kicks), and, of course, lined itself up nicely to place Saturn between itself and the Sun and snap that wonderful picture.
* Humility: In case you don't read the description provided by NASA, that spec of dust on the left side of the photo, just above and outside the brightest rings, is the first planet discovered by man, although it took us thousands of years from the time we first named it until the time we realized it was anything like the other planets. That spec of dust, of course, is the pale blue dot we call home.
For those who won't follow that last link, you owe it to yourself to read what Sagan said about that pale blue dot, even without a giant planet in the foreground to make it seems even smaller:
Look again at that dot. That's here. That's home. That's us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. The aggregate of our joy and suffering, thousands of confident religions, ideologies, and economic doctrines, every hunter and forager, every hero and coward, every creator and destroyer of civilization, every king and peasant, every young couple in love, every mother and father, hopeful child, inventor and explorer, every teacher of morals, every corrupt politician, every "superstar," every "supreme leader," every saint and sinner in the history of our species lived there - on a mote of dust suspended in a sunbeam. The Earth is a very small stage in a vast cosmic arena. Think of the rivers of blood spilled by all those generals and emperors, so that, in glory and triumph, they could become the momentary masters of a fraction of a dot. Think of the endless cruelties visited by the inhabitants of one corner of this pixel on the scarcely distinguishable inhabitants of some other corner, how frequent their misunderstandings, how eager they are to kill one another, how fervent their hatreds. Our posturings, our imagined self-importance, the delusion that we have some privileged position in the Universe, are challenged by this point of pale light. Our planet is a lonely speck in the great enveloping cosmic dark. In our obscurity, in all this vastness, there is no hint that help will come from elsewhere to save us from ourselves. The Earth is the only world known so far to harbor life. There is nowhere else, at least in the near future, to which our species could migrate. Visit, yes. Settle, not yet. Like it or not, for the moment the Earth is where we make our stand. It has been said that astronomy is a humbling and character building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known.
American Heroes
This year's Nobel Prizes have been announced. Citizens of the United States have earned 4 of the 6 prizes, including all 3 (hard) science prizes. These 5 individuals should be known and admired by all Americans, but most of us don't even know their names, let alone what they did. I'm going to do what I can to remedy that.
The 2006 Nobel Prize in Physiology or Medicine: Andrew Z. Fire and Craig C. Mello for their discovery of "RNA interference [PDF]—gene silencing by double-stranded RNA." It should be easy to remember these guys' names; what goes better together than Fire and (marsh)Mello? Yeah, I know it's lame, but you'll remember these two for a while now. What did they do, exactly? They figured out that adding essentially "backwards" copies of genes that are being made into proteins to a cell causes the cell to stop making those proteins. This helped explain some things we didn't understand, and opened up several new possibilities for therapy and research. Their technique is helping us figure out exactly what genes do, and could also be used to turn off genes that are doing bad things. This is all kinds of neat, so remember: Fire and (marsh)Mello!
The 2006 Nobel Prize in Physics: John C. Mather and George F. Smoot "for their discovery of the blackbody form and anisotropy of the cosmic microwave background radiation." Basically, they devised and carried out experiments using NASA's Cosmic Background Explorer (COBE) (well, and, to be clear, led the devising of COBE itself). These experiments led to a greater understanding of the events near the Big Bang, the beginning of the universe. Their map of the cosmic background radiation—essentially the leftovers of the Big Bang—helped us understand a bit more about how galaxies and stars form. So, here's their mnemonic: while they mapped fluctuations in the background radiation, these fluctuations are tiny, on the order of a hundred-thousandth of a degree. In other words, their map is rather smooth, or Mather Smoot. Wow, that might be even cornier than the last one!
The 2006 Nobel Prize in Chemistry: Roger D. Kornberg "for his studies of the molecular basis of eukaryotic transcription." His father, Arthur Kornberg, won the 1959 Nobel Prize in Physiology or Medicine (with Severo Ochoa) "for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid." The neat thing about this one is that Roger essentially helped to finish the work of his father. In cells, generally speaking, DNA stores information, RNA is used to make "working copies" of that information, and proteins are used to do the actual work of running the cell. DNA is copied into RNA, and RNA is translated into proteins. Arthur Kornberg helped figure out how cells make DNA and some of the basics of how that DNA is copied into RNA, and Roger D. Kornberg helped figure out how eukaryotes (non-bacteria, including most everything you think of as alive, from yeast to flowers to humans) transcribe (copy) DNA into RNA. I'm going to take an easy way out on this one: my mnemonics for these great minds are corny, doubly so when we're trying to remember the two Kornbergs!
Fire, Mello, Mather, Smoot, and Kornberg. Remember them. Treat them, and the other unsung scientists that are working to make the world a better place, as the heroes that they are.
The 2006 Nobel Prize in Physiology or Medicine: Andrew Z. Fire and Craig C. Mello for their discovery of "RNA interference [PDF]—gene silencing by double-stranded RNA." It should be easy to remember these guys' names; what goes better together than Fire and (marsh)Mello? Yeah, I know it's lame, but you'll remember these two for a while now. What did they do, exactly? They figured out that adding essentially "backwards" copies of genes that are being made into proteins to a cell causes the cell to stop making those proteins. This helped explain some things we didn't understand, and opened up several new possibilities for therapy and research. Their technique is helping us figure out exactly what genes do, and could also be used to turn off genes that are doing bad things. This is all kinds of neat, so remember: Fire and (marsh)Mello!
The 2006 Nobel Prize in Physics: John C. Mather and George F. Smoot "for their discovery of the blackbody form and anisotropy of the cosmic microwave background radiation." Basically, they devised and carried out experiments using NASA's Cosmic Background Explorer (COBE) (well, and, to be clear, led the devising of COBE itself). These experiments led to a greater understanding of the events near the Big Bang, the beginning of the universe. Their map of the cosmic background radiation—essentially the leftovers of the Big Bang—helped us understand a bit more about how galaxies and stars form. So, here's their mnemonic: while they mapped fluctuations in the background radiation, these fluctuations are tiny, on the order of a hundred-thousandth of a degree. In other words, their map is rather smooth, or Mather Smoot. Wow, that might be even cornier than the last one!
The 2006 Nobel Prize in Chemistry: Roger D. Kornberg "for his studies of the molecular basis of eukaryotic transcription." His father, Arthur Kornberg, won the 1959 Nobel Prize in Physiology or Medicine (with Severo Ochoa) "for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid." The neat thing about this one is that Roger essentially helped to finish the work of his father. In cells, generally speaking, DNA stores information, RNA is used to make "working copies" of that information, and proteins are used to do the actual work of running the cell. DNA is copied into RNA, and RNA is translated into proteins. Arthur Kornberg helped figure out how cells make DNA and some of the basics of how that DNA is copied into RNA, and Roger D. Kornberg helped figure out how eukaryotes (non-bacteria, including most everything you think of as alive, from yeast to flowers to humans) transcribe (copy) DNA into RNA. I'm going to take an easy way out on this one: my mnemonics for these great minds are corny, doubly so when we're trying to remember the two Kornbergs!
Fire, Mello, Mather, Smoot, and Kornberg. Remember them. Treat them, and the other unsung scientists that are working to make the world a better place, as the heroes that they are.
Wednesday, September 27, 2006
Amateur Science
A couple weeks ago, I was talking to someone about the research I did in grad school. Briefly, my research involved computer-aided design of antibodies. While describing my research, I realized that the things I worked on using a relatively powerful computer and high-end software a mere 5-10 years ago could now be accomplished on a cheap home computer, most of it using free software.
I've often thought about going back to grad school, but this realization pointed me to an interesting possibility. Why not try some computational research on my own, self-funded, to see if I could get a research paper published?
The first thing I thought to try was something I had thought of at the end of my time in grad school. One of the big mysteries left in biology is how proteins fold. If proteins simply sampled the possible shapes which they could fold into one at a time, it's said that it would take longer than the age of the universe for a typical protein to fold. But within a cell, proteins fold into their proper shape within milliseconds, or, at longest, hours. And the shape of proteins is important; it's what determines what they do in cells, and what proteins do is what determines what living things do. Another important note on all this is that the sequence of amino acids in the protein determines the final shape of the protein.
One thing that's likely to happen during protein folding is that certain parts of the protein quickly fold, and this quick folding brings other parts closer together, which then interact to fold the protein into its final shape. So, I thought it would be interesting to search through the known protein structures, and see if any short sequences of amino acids --say, combinations of 3 amino acids--tend to have a standard shape in these known proteins. With 20 possible amino acids, and 3 positions, that comes out to 20 * 20 * 20 = 8000 possible 3-amino-acid combinations. It's a lot of things to check, but that's what computers are good at.
So, before starting on this project, I decided to check PubMed to see what had been done since I looked into this in 2000 or so. And, of course, in December of 2002, somebody published a paper about exactly what I was planning to do.
So, that one was out (well, mostly; I still think I might give it a try, but just as an exercise in programming and to test the replicability of their data). While I was at PubMed, I decided to poke around and see if any other ideas fell out.
So then I started thinking about evolution. I started thinking about the human genome. The human genome contains about 3 billion DNA base pairs. New DNA gets into the human genome through two routes, as far as we know: duplication of existing DNA (through things like copying errors or transposons), or incorporation of viral DNA into the genome (something called lysogeny). By tracing the relationships between these genes, using the same techniques we use to trace relationships between genes in different organisms, it should be possible to trace the evolutionary history of every gene in the human genome (with the possible exceptions of the virally introduced genes and genes that diverged too long ago for us to recognize their relationship). I thought that would be an interesting thing to try.
So, of course, did several other people. For example, this mob worked together to map human chromosome 18. Others have done similar things on other parts of the human genome. Not only had people beat me to the punch again, but the job was way harder than my computer is likely to be able to handle.
So... I'm still not sure exactly what I'm going to look into. I still plan to do this, but I've decided the first step is to read a bit more to catch up. If you know of any computational biology work that it might be interesting to look into, feel free to tell me about it in the comments.
I've often thought about going back to grad school, but this realization pointed me to an interesting possibility. Why not try some computational research on my own, self-funded, to see if I could get a research paper published?
The first thing I thought to try was something I had thought of at the end of my time in grad school. One of the big mysteries left in biology is how proteins fold. If proteins simply sampled the possible shapes which they could fold into one at a time, it's said that it would take longer than the age of the universe for a typical protein to fold. But within a cell, proteins fold into their proper shape within milliseconds, or, at longest, hours. And the shape of proteins is important; it's what determines what they do in cells, and what proteins do is what determines what living things do. Another important note on all this is that the sequence of amino acids in the protein determines the final shape of the protein.
One thing that's likely to happen during protein folding is that certain parts of the protein quickly fold, and this quick folding brings other parts closer together, which then interact to fold the protein into its final shape. So, I thought it would be interesting to search through the known protein structures, and see if any short sequences of amino acids --say, combinations of 3 amino acids--tend to have a standard shape in these known proteins. With 20 possible amino acids, and 3 positions, that comes out to 20 * 20 * 20 = 8000 possible 3-amino-acid combinations. It's a lot of things to check, but that's what computers are good at.
So, before starting on this project, I decided to check PubMed to see what had been done since I looked into this in 2000 or so. And, of course, in December of 2002, somebody published a paper about exactly what I was planning to do.
So, that one was out (well, mostly; I still think I might give it a try, but just as an exercise in programming and to test the replicability of their data). While I was at PubMed, I decided to poke around and see if any other ideas fell out.
So then I started thinking about evolution. I started thinking about the human genome. The human genome contains about 3 billion DNA base pairs. New DNA gets into the human genome through two routes, as far as we know: duplication of existing DNA (through things like copying errors or transposons), or incorporation of viral DNA into the genome (something called lysogeny). By tracing the relationships between these genes, using the same techniques we use to trace relationships between genes in different organisms, it should be possible to trace the evolutionary history of every gene in the human genome (with the possible exceptions of the virally introduced genes and genes that diverged too long ago for us to recognize their relationship). I thought that would be an interesting thing to try.
So, of course, did several other people. For example, this mob worked together to map human chromosome 18. Others have done similar things on other parts of the human genome. Not only had people beat me to the punch again, but the job was way harder than my computer is likely to be able to handle.
So... I'm still not sure exactly what I'm going to look into. I still plan to do this, but I've decided the first step is to read a bit more to catch up. If you know of any computational biology work that it might be interesting to look into, feel free to tell me about it in the comments.
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