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October 2008
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corvi [userpic]
Uh... yeah.

I am writing an astrobiology paper on the origin of life - silicon/carbon templating, autocatalytic RNA, pre-organic life. It goes roughly like this, but with more equations and citations of relevant work in it (boring as hell, you probably wanna skip it). I think I'm going insane:

Once upon a time, a long long time ago, before corvi was born, before even ancient people like vix and randomdreams were born, way back in the stone age, before there was a stone age, before there was anything but stone and storm and sea and sun, there was a clay crystal named Michael Montmorillonite. If he had any friends, they would have called him Mike, so we'll call him Mike, because everybody needs friends!

Mike lived with hundreds of other members of the Montmorillonite family in a big sandstone rock. Have you ever seen sandstone, kids? It's made of tiny grains of sand that got turned into rock by the magic of the Sedimentary fairy, but between all those grains in the rock are tiny little caves! Those caves are just perfect for crystals like Mike to live in! Hundreds of Montmotillonites lived there in the tiny little caves, and they were very cozy indeed.

New crystals were born all the time, but animals hadn't evolved yet, so there was no stork to bring the baby crystals, so they were born in a very special way. The sandstone caves were full of sea water, and just like fizzy bubbles in soda pop, the sea water was full of the tiny little pieces crystals are made out of. And the tiny little pieces, when they found a crystal, attached themselves in the perfect place to the side of it, and then another piece would attach to the right place for that so that each new crystal was the same shape as the one it grew on. That's the way crystals work, and that's why sugar crystals are always cubical!

Now, most of the crystals were very very pretty. Mike had a sister named Melinda Montmorillonite. Her faces were perfectly formed, her edges were knife-sharp and glittered with diamonds, and her angles were so exact you could have set the foundation of the universe by them. She was perfectly square, and all her children fit together around her perfectly like puzzle pieces.

But poor Mike wasn't very perfect at all! When he was just a baby crystal starting to grow, he made a very special friend called Helen Hydroxyl. Henry and Helen lived right next to eachother and were best friends. But unfortunately, Helen thought it was funny to make Mike always lean to the left, so that he wasn't all perfect like his sister Melinda. When Mike had kids, all the tiny pieces in the water that attached to Mike had to lean left, too. And then Helen's sisters Henriette and ... uh... Hippolyta (I can't think of another H name. I would be a lousy children's story writer!) thought Mike and his children were just perfect, and came to live with them! And Henriette made some of Mike's children lean, and then more Hydroxyls joined Mike, and so Mike and all his children grew, not into perfect puzzle pieces, but into long, curving tubes because they all leaned towards eachother.

All the other crystals made fun of Mike and Helen because they didn't look right at all. They didn't have sharp edges, and they didn't fit together like puzzle pieces, and they had all those strange foreign Hydroxyl friends. Crystals, you see, are so sharp and pointy they can't be very nice.

But one day in the happy sandstone Montmorillonite home, there was a problem! Melinda and her children, who all fit together like puzzle pieces, had grown completely across their cave, like a wall of bricks! There was no way for water to get in to them, and there was no way more baby crystals could be born! But Mike and his children did not fit together, and they kept growing, and soon there were more of them than anyone else in the caves! And mean old Melinda fell apart into tiny pieces, and the pieces joined Mike, and he kept growing, still! All because he wasn't perfect.

Mike kept having more children. Mike had soooo many children they filled up the entire cozy caves that one day one of them was born outside the cave entirely! His name was Marty. Marty and his friend Haakura Hydroxyl were in a strange new place no Montmorillonite had ever been in the open sea before. And then they saw a strange new creature: Cyndi Cyanide! She came swimming up and said, "Who are you?"

"I'm Marty Montmorillonite and this is my best friend Haakura Hydroxyl. We are a crystal that grew from that rock. Who are you?"

"I'm Cyndi Cyanide, and a big thunderstorm made me!"

"Do you want to live with us?"

Cyndi said, "Sure! I'll just hold onto Haakura." And then the next day Cynthia Cyanide joined them. And then Cyndi and Cynthia smooshed themselves together and turned into Rachel Ribose. And they all lived together happily, even though Marty's family all thought he was strange for befriending Cyanides and Riboses. And Marty had children, and the children made more new friends in the Sea. But there were so many Riboses that they started calling it Ribose-Home, and shortened to it Ribosome. And the Riboses invited all their friends and all their friends held onto Haakura and Marty's children around the edges. Which was good, because it protected Marty from being broken. So he grew even faster, and there were more and more Riboses. And there were so many of them that they were lined up perfectly, all touching eachother.

And then the Riboses were lined up so perfectly that they didn't need Marty's help any more, and they went off and evolved into RNA and carbon-based life and you and me. And they laughed at those stupid crystals the whole time. So should you.


Okay, yes, I think I can say with surety I am insane. And boring, too! That said: the concept of 'genetic takeover' is really fascinating. The genetic molecules all known life uses are really, honestly, too complicated to have evolved by chance just from lightning and sea and lava and such. There are several explanations as to how this could have happened, what the 'missing link' is. My personal favorite (and, in my opinion, the most plausible, which isn't saying much) says that complex crystals acted as 'templates' for RNA, which then catalyzed DNA eventually.
The crystals would have had to *evolve* - different impurities or structural defects would have worked out better in different locations, and more of the imperfect crystals would have grown. Evolution. Life of a sort - silicon based, instead of carbon-based. Their 'genes' would be geometric, not chemical - structural flaws that would be passed on to the children of the crystals. They would have eventually started to incorporate organic molecules like cyanide, which would have served "useful" functions - making the matrix harder or more flexible or what-have-you. The exact effect depends on the exact organic involved. Evolution in action, and all. Bet evolving crystals would give Darwin nightmares.
These critters would have continued to get more complex, building more complex organic structures, as well. Until the organic structures began to take over more and more of the function of the creatures. Eventually organic systems complex enough to make more of themselves evolved, and carbon-based life replaced silicon-based life. This is referred to as 'genetic takeover'.

I don't want to write a paper about it. I want to write a science fiction story about some planet where it never happened! Though I have to admit strange children's stories are fun, too.

Current Mood: evolving
Current Music: Revolutionary Girl Utena - Paleozoic Within The Body

hee hee... i didn't understand half of the biochemistry here, but its a great story!

you should seriously consider going into the children's storybook writing business.

Actually, this probably would have come out as a random rant (and I would have deleted it before posting it) had you not posted a couple of days ago about The Cutie Bunch Friendly Pal Pack. I don't think I would have thought of a children's book otherwise; even as a child, I did not read them. So thanks for the compliment, and thanks for inspiring me.


oh, my! its all my fault! how cool.

you never read children's books as a kid? did you skip Good Night Moon in favor of Biochemistry for the 10th Grade, or what?

This was absolutely delightful!
Thank you.

Hee! I really thought that would bore the hell out of everyone. Glad you liked it!

Well, actually, I added it to my memories. So, yes, I liked it. :)

Have you studied chemistry? I've realized I really don't know what you do...

I have studied chemistry in the past and I'm familiar with at least the basics. I know what I'm looking at when the molecular solid screensaver comes up. I could probably solve a covalence equation with a little bit of work.
But I tend to study physics a lot more...

As for what I do:
I learn. I chat. I study and watch people. I disturb people's reality grids.

If you mean what do I do for pay, I am a Perl Programmer and LDAP Administrator.

So, how about yourself?

I must confess to being a fairly uninteresting college student. Studying computer science. Odd jobs such as students hold - tutoring, research, translation, codemonkey. Dietary intake >30% ramen. That sort of thing.

What about the electives? Anything interesting there?
If your diet was significantly ramen-ised, would you really be a student?

This quarter, the electives are Medieval Celtic History and Culture and Honors Astrobiology. Unsure whether they're interesting. I like to think the fact that I'm deliberately digging in my heels and not graduating so I can test a specially designed robot in freefall with NASA next year is at least minimally interesting, though. At least, it is to me.

(Note to self: post robot demo pictures.)

Courses like that sound interesting. What is Astrobiology anyway?

so, when are you going to post the robot demo pictures?

Astrobiology is technically the study of life on other planets.
Obviously, since we haven't discovered life on any other planets yet, it's currently a highly theoretical science. It involves some astronomy (What kind of star has planets? What kind of planets could life exist on?), some biology and biochemistry (Well, how does life on Earth work, exactly? Would it work on Mars?), some geology (Volcanos? Undersea vents? Fossils?).
It's a lovely mess of studying the solar system and lots of scientific what-ifs and the truly wierd little creatures who live in boiling hot water around undersea volcanos - entire ecosystems set up in sulfur and magma and no sun- and the moons of Jupiter, and occaisional wild flights of imagination. Lots of fun.

Wow. I must be much tireder than I think. I have no memory whatsoever of writing that response; furthermore, I had been under the impression I was asleep with my forehead on the keyboard at the time indicated. Scary.

/me is highly amused at sleepwriting...

So, astrobiology seems like the coolest class ever. I wish GMU had offerred it. The closest I've ever come is the planetbuilding seminars that have occurred at some science fiction conventions. Some of these have been better than others. Do you have a course book? What sorts of conclusions are you coming to? Learn anything unexpected?

I took an astronomy course where the prof had been teaching the same course for 15 years and had written the book we were using. All of his classes were the same and you could point to the paragraph he was teaching from.

Remind me that I need to post the new robot pictures soon; well, as soon as I'm home and have access to broadband again.

Everything else is at http://depts.washington.edu/gyre/gallery/ though.


DNA is very similar to RNA. It's more expensive to make but it's vastly more stable. Proteins, while singly simple, are intensely complicated once you've got a bunch all packed together. The discovery that under some conditions, RNA assemblies could catalyze reactions, which was previously thought to be purely a protein job, won a Nobel prize and pointed some big fingers towards our past.
The idea of topological replication, a mutant protein promoting production of more copies of itself, not only pushes the idea of evolution along pretty well, but also explains why mad cow disease works so amazingly well on all sorts of unrelated animals.
If you take soap-like molecules and shake them in water, you can form these things called micelles, which (probably not coincidentally) are nearly identical to cellular membranes.
If a cell ingests a very primitive bacterium, and the bacterium actually ends up slowly replicating inside the cell, and eventually they become codependent, you might call the ingested material mitochondria.
Or if you're a plant, you might call some of them mitochondria and others chloroplasts.
And in the end, the closer you look, the fuzzier the distinctions between different species, families, and kingdoms get. We're all just glop, madly self-amplifying glop.

An online conversation with tithonium that amused me:

Martian says to corvi, "I like the story, but the ending seems a little sudden."
corvi asks of Martian, "but the ending is the best part! did you know there was montmorillonite on Mars?"
You say, "*lots* of it. they think it may be what's responsible for some of the viking lander's bizarre results."
corvi says to Martian, "which is why i named the RNA-template crystal after
corvi <- one big inside joke
corvi <- one big dork, too
Martian appreciates that.
Martian takes a shiny ruby bead from his pocket and gives it to you.

That's lovely!

I've come across this sort of theory once before, in a Dawkins book. It's really interesting, though I'm in no position to judge plausability.

Since you like origins, are you familiar with the Aquatic Ape Theory?