Friday, September 30, 2011

"Tevatron atom smasher shuts after more than 25 years" - BBC

Tevatron atom smasher shuts after more than 25 years

Another blow for American scientific research, both in the U.S. and the rest of the New World.  The Tevatron is/was the second most powerful particle accelerator in the world, operated by Fermilab, and it smashed atoms together at near-light speed right here in the midwestern United States.  And it will be shut down for good possibly by the end of the day today.

This comes after news in April that SETI, the project to listen for extra-terrestrial radio signals, halted operations, and lacks the funding to continue.

Both of these examples have something in common:  they're extremely difficult-to-defend scientific projects.  People don't know what the point is of smashing atoms together to try to see the bits that come off, or listening for a signal that might never come, and would take decades, centuries, or longer to send a message back if one ever came.  I'll admit, sometimes I don't know what the point is either.  But then I remember something.

Two centuries ago, people knew what electricity was.  Well, some people did.  It was used in scientists' labs to make frogs' legs switch.  It was used at fancy parties to give people a little shock or tingle, or make their hair stand up.  You could see little sparks go from one electrode to another.  It was a quaint little party trick, but nobody could really imagine any use for it.  Less than a hundred years later, electric light was powering a city street, its utility was proved, and new industries of electric power and electric machines were born.

Electricity was a long shot.  It felt like magic to many people, the same way that the quantum mechanics, the behavior of atoms and electrons, feel like magic to you or me.  The more you learn about atoms, the bits that make them up, and how they interact, the less it all makes sense.  And it seems crazy that you could learn anything useful from trying to study them.

But atoms, like electricity, were studied anyway.  And research in atoms and their properties led us to create a devastating weapon, and a source of relatively clean energy.

And now we live in the "Information Age," where computer processing power translates into real power.  And we got here through engineering breakthroughs, with not much help from the developments in quantum theory (what these colliders are working on) along the way.  But there is talk of "quantum computing" on the horizon, a development based on quantum theory that would revolutionize the computer industry, increasing their processing abilities by orders of magnitude, and making possible calculations that are impossible on current machines.

And SETI, well, listening for space aliens is still a long shot.  We may not hear anything for thousands of years, or ever.  But, what if we do?  What if we catch an alien broadcast?  What would that mean for the world?  Could we get over our disputes and grievances, put an end to petty politics, and finally work together as one humanity toward a common goal of mutual prosperity and expansion beyond the globe?

Well, yeah, that's a bit far-fetched, but it's easy to imagine and might have a pinch of truth to it.
And finally, when you consider the costs of these projects, compared to what it takes to grow our food, power our homes, educate our children, and especially fly our planes and soldiers into foreign countries, funding particle accelerators and radio telescopes and staff to run them is really not so much.  Scientific programs in this country get by with a pittance, but they show amazing results.  And now we seem to be content letting other countries take the scientific helm, as the Large Hadron Collider continues smashing atoms, and China's and India's space programs get off the ground.

I agree that budgets all over the country are in crisis right now, and people are struggling, so I won't push for this over all other causes.  But when we get things sorted out again, let's not forget where science got us, even when it seemed like a waste of time.

Thursday, September 29, 2011

DNA Transcription and RNA Translation

This is an example of one of those moments in my science education where things... just... clicked.  Maybe you know the feeling.

I knew about DNA, RNA, transcription, translation, proteins, the nucleus, molecules, et cetera, et cetera, but this video, after watching it in my high school biology class made everything fit together in a coherent picture.

For me, the realization had a few parts.  First was:  proteins are molecular machines, and everything they can do is based primarily on their shape.  Everything in the video, aside from the double-helix DNA "red" strand, and the single-helix RNA "yellow" strand, is a protein or amino acid, those little red bits that get stuck together to make the deep red hemoglobin protein at the end.  (Since hemoglobin, which uses iron to carry oxygen through the blood, is responsible for the red color of blood, its color in the video might be accurate!)

But those big, chunky blobs throughout the videos are very special proteins that can only do what they do based on their shape.

Now, right at the beginning of the video we saw a bunch of these proteins latch on to the DNA strand, and several had to come together before the work could be done.  On a tangent, this is a perfect example of the "Intelligent Design" irreducible complexity argument.  The argument goes, "Well, see this thing here.  It couldn't work at all if you take one piece away, and if evolution always adds just one piece at a time to a structure, this would be useless until you had everything put together at the end, so evolution wouldn't select for any individual component.  Therefore, an Intelligent Designer/God/magic/a wizard did it!"  In this case, the process can be done by one protein acting alone.  Other proteins can be added to refine the process or speed it up.

My second realization took a bit of extra thought.  I was still confused as to how all these bits and blobs actually came together.  How do they find each other?  The truth is, the video doesn't show everything going on.  It can't.  What you aren't seeing is that big empty space inside the cell and inside the nucleus, is FULL of these proteins, amino acids, nucleic acids, strands of DNA and RNA, sugars, fats, everything!  The video shows a big open space with a few shapes inside working together, but that empty space is a soup of molecules partaking in similar interactions.  The video had to take that out just so you could see what they wanted to show you.

So the second realization was that molecules in your cells don't know what to do, and don't seek each other out, they're just all crammed in there together, they bump up against each other, and they react, based purely on chemical bonds and shape.  And it all just happens on its own purely because it can, and when it does it well it can keep doing it for years and years to come.

Wednesday, September 28, 2011

Bug Books at the Library

Earlier this year, my supervisor at the library where I worked gave me the task of creating and maintaining a book display on any subject I liked.  Well, I had no other option, really, than to choose insects and spiders, did I?

This is a picture of the display right around the beginning of the month of May, when I had just gotten it set up.  The Dewey Decimal system keeps all the insect non-fiction together (number 595.7), so it was fairly easy to find books for the display.  Most of what was on the shelves was focused on local New Mexican and southwestern fauna, like the butterfly book on the upper left, but I was trying for a more eclectic display.  Let me give a quick run-down of the books I had read and wanted to share at the library:

The Life of Insects by Viktor Pelevin (top, center)- This was one of the rare fiction books on this display, and the first on this list I ever read.  I picked it up for the first time, almost at random, while visiting my older brother's college's bookstore.  I was in high school.  I didn't know anything about the author, but the cover and book jacket intrigued me, and it wasn't too expensive.  The book takes place in post-Soviet Russia, following the lives of several people, who are also insects, who are also people.  It's a bit difficult to explain, or imagine, but eventually the book kind of swallows you up and you're along for the ride.  The characters include some mosquito businessmen with a fellow American mosquito going out on a bender of bloodsucking, a dung beetle father explaining all the mysteries of the universe to his dung beetle son, a young queen ant and the perils of domestic life, and a cicada who tunnels his way through life, going to work and home again, and briefly to America where he nearly turns into a cockroach, all while digging, digging, digging in a straight line.  It's a great read.

Life in the Undergrowth by David Attenborrough (center)- A great look at the whole terrestrial arthropod kingdom, told in order of evolutionary descent, with centipedes, millipedes and scorpions in the beginning, and ants (of course!) and bees at the end.  This would be a great coffee table book, really, since it is full of beautiful pictures of all range of insects and spiders.  I learned a lot from this book, and Sir Attenborrough is a wonderful teller of the tale of life.

Clan Apis by Jay Hosler (center, right)- A graphic novel, appropriate for kids and teens, but a great little book for anyone to read.  It tells the tale of a worker bee, from hatching as a larvae to (spoiler alert!) a timely death after a short, but fulfilling life.  It's a cute little story, full of facts about the lives of honey bees and the insect world, and the pictures are wonderfully illustrated.

Insectopedia by Hugh Raffles (bottom, left)- Not as comprehensive as the "-pedia" ending led me to believe, it nevertheless provides 26 stories, in alphabetical order by chapter title, about the nature of the complex and diverse relationships between humans and insects.  There are heartwarming stories as well as revolting ones, most notably the stories of the stomping fetishists, mostly men who enjoy watching women stomp on things, and imagining themselves as the recipient.  (That chapter gets very Freudian.) On a lighter note, I will say that after reading this book I never more wanted to try roasted locusts.  Does anyone have a recipe?

Ants at Work by Deborah Gordon (bottom, center, only spine showing)- I'll just say right now, you could probably skip this book unless you really, really, love southwestern harvester ants and want to know all the nitty gritty details of how their colonies are actually organized and how researchers are finding out.  I learned a lot from this book, but it's not written for a wide audience.  If you do love harvester ants and want to everything about them, this is the book for you!

Parasite Rex by Carl Zimmer (bottom, right)- Last and certainly not least, this book was a great overview of the world of parasites and much more entertaining a read as that sounds.  Zimmer has that much-coveted quality of writing that is easy to read and grossly (har har) informative.  He argues that parasites should not be considered the lazy cheats of the animal kingdom, and should certainly not be ignored as insignificant.  Rather, their adaptations for life within other creatures are impressive, and their impact on the environment can be drastic.

So there you have it.  Unfortunately, the epilogue here is that not many of these books were actually picked up.  (Sad face.)  However, half of the display was devoted to children's books, and those flew off the shelves by comparison.  So books like What to Expect When You're Expecting Larvae got to enlighten young minds, and the display was reorganized to give more space to similar bug-themed picture books.

Tuesday, September 27, 2011

Velvet Ants and Ant Police

While staying up too late last night and browsing my favorite subreddit,r/whatsthisbug, I came across a picture of a bug I actually recognized, the velvet ant.  Now, the velvet ant is not actually an ant, but a relative of all ants and wasps.  The males have wings and often aren't identified easily, but the females, unusually in wasps and ants, lack wings and have bright red or orange fur covering their bodies.  They are a very cool insect to find, but they are said to have one of the most painful stings in the insect kingdom, so whenever I've seen one here in New Mexico, I've never tried to pick it up.

Now, I'm getting sidetracked here, because what I wanted to really talk about was what happened in the discussion of that velvet ant photo.  I don't often chime in to these discussions, because more knowledgeable scientists and bug trackers are usually around to identify creatures down to the genus or species, when I have more of a layman's understanding of arthropods.  But I had to here, because people started talking about ants and ant egg-laying behavior, and ants, as you will know doubt discover while you're here, are my favorite, and there are few books about ants out there I haven't read.