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:
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.

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.

Friday, September 01, 2006

Mysteries of the Explained

One Monday, a chemist was researching the properties of a new explosive. He weighed it carefully, ignited it, and then weighed the product. He was astonished to find that the product weighed more than the starting materials.

"I must have missed something," he said. "Certainly this result is not enough to overturn the well established atomic theory of matter."

He soon realized that he had forgotten to account for the mass of the air, and everyone agreed that it was prudent for him to re-examine his work.

The next day, a physicist was studying transmission of light through a new substance. When he completed his experiments, it seemed that the light was coming out of the substance before it had gone in.

"I must have missed something," he said. "Certainly this result is not enough to overturn Maxwell's electromagnetic field theory."

It took him some time, but finally he found an error in an equation. Everyone agreed that it was prudent for him to re-examine his work.

On Wednesday, a biologist was studying the genome of a bacterium. He was amazed to find that the genome had more similarity to a certain species of fungus than it did to other bacteria, even though he had expected it to be a typical bacterium.

"I must have missed something," he said. "Certainly this result is not enough to overturn the well established theory of evolution through natural selection."

"Just-so-stories!" screamed one onlooker. "The bacterium must have been designed!" shouted another.

Why oh why oh why does the study of biology get such special attention? Scientists make mistakes. More importantly, scientists, even smart ones, are not always right. When they predict something based on a well established theory, and that something turns out to be false, it is prudent to re-examine their work to see what might be wrong before chucking the well established theory. Of course, if it isn't possible to explain the evidence in the framework of the well established theory, or if the explanations require twists and turns that can be more simply explained by some other theory, than even a well established theory can be overturned (for example, it was well known in the 19th century that light propagated through a medium called the "luminiferous aether," but then the Michelson-Morley experiment showed that the aether did not exist, and a new theory had to replace aether).

Evolution is supported by piles and piles and piles of evidence, from molecular biology (both DNA comparisons and protein comparisons) to paleontology (the fossil record isn't complete, thanks to the way fossilization works, but everything in it supports descent with modification) to direct experimental observation (not to mention years of artificial selection, which is just a form of natural selection, in which humanity takes the role of the environment). And, as creationists strangely like to use as an argument, elements of the theory of evolution through natural selection are tautologous, or, as m-w.com puts it, "true by virtue of its logical form alone." Of course the organisms that are more likely to pass on their genes pass on their genes more than the organisms that aren't.

So, when we find a single organism that does something weird, of course biologists attempt to explain it--not explain it away as creationists like to say, but explain it--by fitting it into the framework of natural selection, by figuring out what selective advantage its weirdness gives it. Until someone finds something much, much stranger than anything we've found so far, natural selection is by far the best explanation we have for the diversity-yet-clear-relatedness of life.

Thursday, August 31, 2006

Quick Links

First, everyone watch this. Then tell people you know to watch it. Everyone should see that.

On a far less serious note, I'm now writing this blog using Writely.com, Google's online kick in the balls to Microsoft (which, as a kick in the balls, connects it to my first link). If I make spelling errors, you should report them at Writely.com, since the software is beta. It isn't my fault anymore :-P

Tuesday, August 29, 2006

APOD Shuffle

Random thoughts inspired by NASA's Astronomy Picture of the Day (APOD):

  • Orion Nebula: This picture shows how the Orion Nebula looked 1500 years ago. Or, well, at least how it would look if we could see in infrared. But, really, it's only 1500 years on average. Stuff in the front of the picture sent that light out more recently than stuff in the back. The whole sky works that way. We see Proxima Centauri as it was a mere 4 years ago, while we see the Andromeda Galaxy as it was about 2.5 million years ago. If we somehow constructed a map of where the stars are right now and how bright they are, it would look different than the sky we're used to. Not only would some stars be missing and some new stars be added, but everything is also moving relative to one another. Those things that we see as they were 2.5 million years ago likely are quite a ways away from where we see them, for example.

  • Horsehead-shaped nebula: This beautiful image of a horse's head (not to be confused with the Horsehead Nebula) is also a great example of the strange and interesting phenomenon called pareidolia. Humans are pattern-seeking creatures, so when we look at things, we try to assign them to categories. We look at this nebula, and we see a horse's head. We look at a hill on Mars,and we see a face (and some continue to do so even when a second photo shows that the resemblance in the first photo was coincidental). And, of course, some people look at a grilled cheese sandwich, see a shape that looks vaguely like a human female, and assume it's the Virgin Mary.

  • Lagoon Nebula: Why couldn't whoever runs the APOD at NASA take the 5 minutes to make those two pictures line up (mouse over the picture to see what I mean)? Sigh. Still beautiful.

  • 3D galaxy: It's amazing to me that that's a photo; strangely, it looks too real to me for me to immediately accept that it's really a photo. It's the kind of shot you might create for Star Trek credits or something. That galaxy is about 50 million light years away, but remember: the front edge isn't quite as far away (and therefore not as far in the past) as the back edge. However, compared to the total distance, the 30 thousand light year diameter of the galaxy is almost nothing.

Monday, August 28, 2006

Mapping Human Knowledge

A couple years ago, when the company I work for ramped up work on our homework system, my boss jokingly gave me the task of "mapping human knowledge" to create our topic list. We pawned much of the effort off to the authors working on our authoring projects in an attempt to make things easier, but that turned into a colossal mess.

Tonight, I finished collapsing that mess into a canonical list of chemistry topics.


Sunday, August 27, 2006

Memorizing Very Exact Mnemonics Jeopardizes Science's Updatable Nature

"My very excellent mother just served us nothing. That is not nearly as yummy as nice pie. Darn astronomers stealing Pluto from our solar system."

That was what my sister sent me when she heard Pluto had been demoted from planethood. And, of course, she wasn't alone; many people were upset to "lose" Pluto.

Of course, we didn't "lose" Pluto. It's still out there, orbiting the Sun. You can even call it a planet if you want. All that happened is that the International Astronomical Union, for the first time, defined what a planet actually is, and that definition doesn't apply to Pluto.

Why did they do it? They tried not to. In October, 2005, they were set to define a planet as "Any object in orbit around the Sun with a diameter greater than 2000 km." That was a fancy way of saying, "A planet is Mercury, Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, or Pluto," since at the time they thought Pluto was bigger than all of the "potential planets" that have been discovered in recent years. Of course, that definition wasn't very precise, because the Moon (the one that orbits Earth) also orbits the Sun (if we lived on the Moon, we'd probably think of Earth as another planet sharing our orbit), and, with a diameter of 3500 km, it has no trouble squeaking in.

But then we got a good measurement of Xena. Xena, also known as 2003 UB313, is a ball of ice and rock orbiting the Sun in an orbit similar to Pluto's. Earlier this year, NASA pointed the Hubble space telescope at Xena, and found something interesting. Xena has a diameter somewhere between 2300 km and 2500 km. Pluto has a diameter between 2280 km and 2330 km. Xena is right around the same size as Pluto, and quite possibly bigger.

So why did the IAU eliminate Pluto from their definition of planet? Because they're scientists, and scientists have to deal with the real world, not with how they wish things worked. For the word planet to have any scientific meaning, we have to be able to rationally decide if some object is or isn't a planet. In order to do that, there have to be some sort of measurable criteria. Try as they might, the IAU couldn't come up with a definition that seemed important enough for what we've always meant by "planet," but still included Pluto.

But that's the great thing about science. As we find new information, we continuously tweak our explanations to match the data. As time goes by, and we get more information, we refine our predictions and explanations to make sure they still hold up. We constantly update what we think we know to match what we observe.

This is what allows us to make progress. This is why I'm able to write a blog on a computer that communicates through the rest of the world through the air, rather than writing letters that take months to cross the ocean. This is why we now have bathrooms in our houses, rather than in the yard. This is why babies dying at birth is a rare event now, rather than the norm.

And that's why now we know that we have eight planets in our solar system, plus at least three dwarf planets. That's the thing people seem to be missing. We didn't lose Pluto. We gained 3 dwarf planets (besides Pluto, one was formerly an asteroid, and the other was formerly one of those things that we didn't have a name for before). We gained slightly better understanding of the solar system in which we live.