Wednesday, May 30, 2007

Origins of Life: Slightly Less Mysterious

The best 'Fundies Say the Darnedest Things' EVER, in which a Creationist almost discovers the Sun:

"One of the most basic laws in the universe is the Second Law of Thermodynamics. This states that as time goes by, entropy in an environment will increase. Evolution argues differently against a law that is accepted EVERYWHERE BY EVERYONE. Evolution says that we started out simple, and over time became more complex. That just isn't possible: UNLESS there is a giant outside source of energy supplying the Earth with huge amounts of energy. If there were such a source, scientists would certainly know about it. [emphasis added]"
But the Sun isnt the only energy source available to life on this planet! Dont forget the 'fire' below our feet, and the science that can happen where that energy is released-- Like at hydrothermal vents on the bottom of the ocean!

Thermal vents' place in abiogenesis didnt totally make sense to me before. I was thinking of their potential contribution as like, a natural PCR machine. When DNA is close to a thermal vent, the high temperature causes the double-stranded DNA to 'melt' into single-stranded DNA. As the ssDNA rises via convection through the thermal column, DNA replication machinery can get in to replicate the ssDNA into dsDNA. Floats down, gets close to the thermal vent again, and the process happens again! Lots and lots of copies! Neato!

Well, um, yeah that 'makes sense'... but it leaves more questions than it answers. Where the hell did the first DNA strand come from? Whered all the replication machinery come from? Whats keeping everything contained? Huh??

Leave it to the folks at NAS to turn a kinda weird idea up on its head and twist it into a viable hypothesis. They go back further than DNA. Further than the RNA World. They go back and try to explain the development of the RNA World itself!

Extreme accumulation of nucleotides in simulated hydrothermal pore systems


hehe So in other words, forget everything I just typed about thermal vents and DNA!

Just picture a hydrothermal vent: a chimney through the earth. But this chimney is composed of a maze of iron-sulfide compartments instead of bricks (is, not maybe, these still exist today). When combined with the energy from the hydrothermal vent, this maze acts like a sieve, first collecting mononucleotides. The nucleotides utilize the abiotic catalysts in the iron-sulfide rock (FeS and NiS) to generate strings of nucleotides: RNA (in their experiments, Baaske easily get strands ~100 bp long this way). As the strands are pushed further away from the thermal vent by convection, the temperature lowers enough that the strands are able to ligate to one another and recombine, exploring the sequence space (all possible base-pair combinations) even further.

This essentially allows hydrothermal vents to turn into little RNA factories! Every possible impossible RNA sequence can be tested. Invented, lost to degradation, and invented again! Impossible events happening all the time! Ribozymes, polymers, replicases, tons of stuff! Abiotically!

Alas, always remember your assumptions! What are these folks needing to assume? The presence of mononucleotides. Drat! The answer to life, the universe, and everything still remains elusive. But as the PNAS commenter so aptly put it:
"...the transition from a solution of small organic molecules to a population of RNAs, now appears much less mysterious than before."
Edit 5/31/o7-- Head over to VWXYNot? for more tricks RNA can play!


Tyler DiPietro said...

Every once in a while I get jealous of you bio-folks. Other than cosmologists and astrophysicists you people seem to be tackling some of the most profound phenomena in the universe! It almost makes me want to stop floating around the world of abstract math and get into a lab. Almost...

Foxy said...

That's just damn awesome.


Just like abstract math, btw.

Dustin said...

Hey ERV, this is off topic, but I could really stand to feed off of your clout like a giant tapeworm.

Please please please get out there and spread that link like HPV.

Logan said...

ERV, you should look into the new Scientific American (at least the one that was on the shelves in May). It has an article about a hypothesis for a "simpler" evolution of life that may get it up to the point where it can be taken on by hydrothermal vents.

It basically postulates a "metabolism-first" model instead of a "replicator-first", in which the first bits of "life" are defined thermodynamically rather than genetically, as isolated areas of decreased entropy that perpetuate, adapt, and evolve before achieving replicator status.

Tyler DiPietro said...

"Just like abstract math, btw."

Nah, abstract math sucks pretty bad. I'm pretty sure I should commit seppuku in the lobby of my university campus for choosing it as my undergrad major (or at least one of them at this point).

VancouverBrit said...

Cool stuff. The first time I heard about the RNA world hypothesis it just blew my mind. Molecules that can store information AND have catalytic function??!! I think that was when I made the final step and realised that there really was a 100% natural explanation for the origins of life on Earth with no need for any other explanation. It just suddenly made sense.

ERV said...

hehehe Dustin, I have a clout of four, but I shall try!
Heres your link because Blogger cut it off (I love Blogger) The military is hoping to bomb a valuable fossil site and priceless historical artifacts. Go USA! Ugh.

Logan-- I saw that! I gotta go to the library tomorrow to make a copy!

Vancouver-- I know. And when you add in the neat tricks viruses can do, little pirate ships, shuttling genes around... Reality is so much cooler than any of the Creation stories people have thought of.

ERV said...

One more try on the link.


Torbjörn Larsson said...

Since I just recently understood the niftiness of iron-sulfide catalytic surfaces elsewhere in abiogenesis (rather largish FeS surfaces are assembled in simple organic catalysts, suggesting possibility for early function) I found this especially interesting.

Davis said...

"Nah, abstract math sucks pretty bad."

Get out while you still can! (I'm mostly kidding.)

Whenever I read about research like this, I get science-envy. Sometimes I'm seriously tempted to do grad school again, this time for biology.

ERV said...

Hey guys-- I was raised by a math teacher. I shall have no math-bashing on MY blog!

You know what I hate about bio? There are a lot of people who appear to just be floating through biology grad school, not pushing themselves as post-docs... Im like, "Are you people INSANE??" There is so much cool stuff going on, how can they NOT be excited about it??

The next time I catch one being particularly lazy, Ill scold them with "Do you have any idea how many mathematicians would love to be doing what youre doing?"


Im kidding-- I appreciate the contributions of mathematicians in the protocols and technology I use. Hell, this paper were so excited about wouldnt have happened without mathematicians.

Davis said...

"I shall have no math-bashing on MY blog!"

Forgive me if it sounds like I'm bashing math. I'm just frustrated by the current state of the job market for abstract mathematicians. :P

ERV said...

Oh Im just kidding too :)

If its any consolation, the market is bad in biology too. You know the economy is in the crapper when the HIV and cancer researchers are having trouble getting grants. I dont know how the ecology/NSF guys are doing it in this political and economic environment. Ugh.

And I can imagine its exponentially worse for you guys :(