Friday, January 20, 2012

Where Did DNA Come From?

Crankiness that comes with chronic sleep deprivation and resulting need for weapons-grade stimulants aside, I'm a pretty easygoing dude.  Still, mentioning that you don't believe in evolution (or worse, that you "think there are some holes in the theory") within earshot of me is a great way to get a quick crash course in all the swear words I know, as well as the myriad ways to connect them together that I've come up with over the years.  Part of it is a general irritation with people who decide science isn't true because they don't understand it (I have similar reactions to global-warming deniers, people who don't vaccinate their children, and everything Deepak Chopra has ever said), but it goes a bit beyond that because, as tools for understanding the world around us go, you really aren't going to do a whole lot better than the theory of evolution.

Somebody (I think it was Einstein, he was always saying smart stuff when he wasn't denying that quantum mechanics was true) said that the value of a scientific theory can be quantified by how good a predictive model it is divided by how much effort it takes to get said predictions out of it.  By that metric, evolution beats everything out there: the essentials of it can be summed up in a paragraph at most, and armed with just that paragraph (no calculus! yay!) and basic logic you can work out everything from why night predators don't have infrared vision to how the platypus came about.  Anyone who has ever tried to talk someone who hasn't taken grad-level physics through quantum mechanics, general relativity, or (godforbid) the standard model can appreciate that.

Unfortunately one of the major consequences of evolutionary theory is that people, with all their brainpower, personalities, nice racks, etc, aren't much more than highly-optimized delivery mechanisms for their genetic information.  Walking, talking seed packets, if you will.  Quite understandably, this is upsetting to a lot of people, some of whom respond by pretending evolutionary theory is "controversial" and forcing dumb shit like "intelligent design" to be taught to Texas schoolkids who don't know any better.  In reality, evolution is about as controversial as gravity; if you don't believe me, go contract one of those lovely MRSA strains that seem to have worked out how to defeat every single one of our antibiotics.  Not only is it utterly noncontroversial, it's also absolutely fundamental to any understanding of modern biology (and, interestingly, some computer science); trying to do, for example, immunology without a solid understanding of evolutionary theory would be like trying to read Shakespeare without knowing the alphabet.

Rick Santorum, inadvertently making the case against intelligent design

People who don't particularly like evolution usually resort to attacking it by pointing to things in nature with "irreducible complexity;" that is, complex things like the eye that don't seem like they'd confer any evolutionary advantage until all their parts were in place, as proof that there's more than the blind statistics of natural selection at work in creating biodiversity.  Aside from being a logical fallacy masquerading as an argument (not understanding something isn't the same thing as it not being true), it's usually pretty easy to come up with stepwise models for how even complex organs like the eye could have evolved from, say, a single cell with a mutation that made it slightly light-sensitive.  The one place I've always gotten hung up, though, is in trying to explain where DNA, which is one of the main ingredients needed for natural selection to work, came about.

In order to get natural selection to happen, you need three things: a way to transfer information between subsequent generations (that'd be DNA), selection pressure (an environment that ensures that some individuals will be more likely to reproduce than others), and a randomization factor so new things keep getting tried out (that'd be genetic mutation).  Start with those three things and you can go from a single cell to an elephant, although it'll take awhile (one thing evolution is not is efficient).  The crux of the problem here is that without all three of these things, you've got no natural selection, leading to a bit of a chicken/egg problem.  Selection pressure and randomization are easy (any environment is going to exert some degree of selection pressure, and pure statistics will give you "bad copies" every once in awhile if you're working at the molecular scale), but how did we get a molecule that can hold an assload of information and the associated, unbelievably complex cellular machinery needed to both translate that information into proteins (which are themselves so complicated that we need supercomputers just to predict their morphology) so it can do things as well as allow it to self-replicate?  There's a lot of infrastructure there, and contrary to what the God-botherers will tell you it didn't all just pop into existence at once.  Or did it?

The answer is no, it didn't, and if I knew more about basic chemistry and biology (disclosure: I'm way outside my science comfort zone here, so the following explanation is going to be a bit sketchy.  I'm doing my best though) I'd have been able to reason this one out for myself the way I usually can with any complex evolutionary result.  The secret is that the complicated DNA/RNA/protein system we use as the basis for our genetics itself evolved from a series of similar, but much simpler and less effective, information-transfer systems.  The prevailing theory for how it all came about is called the "RNA World Hypothesis," and it's been backed up by a lot of really rigorous experimental and theoretical work and is pretty universally accepted. 

So let's go back to early planet Earth.  It wasn't a very exciting place, mostly just rocks, lava, a corrosive and mostly poisonous (to humans) atmosphere, and a primordial soup of miscellaneous organic molecules.  Miller's famous experiment from the 50s showed that said primordial soup could originate from a combination of methane, hydrogen, ammonia, and water, catalyzed by an electric discharge, so the idea that there were these pools of "probiotic soup" lying around isn't really that far-fetched.  This soup mostly sat around reacting with itself for awhile, producing useful stuff like fats and amino acids.  Eventually, via one of several possible reaction paths, a handy little molecule called ribonucleic acid (RNA) turned up.

RNA is kind of the beta-test version of DNA (and, like most beta code, bits of it can still be found floating around in the current version of cellular mechanics).  Like DNA, it's a long-chain molecule with a bunch of amino-acid bases attached in a specific order.  Unlike DNA, it lacks a double-helix structure, instead opting for a much less chemically stable single-strand morphology.  That's useful in this case though, because it means RNA can catalyze reactions as well as store information-- something DNA can't do without a lot of supporting apparatus.  Since RNA is reactive, it's going to interact with the other stuff in the prebiotic soup a lot, including via something called a "replication reaction" where the dangling amino-acid bases of the RNA chain essentially help it assemble a mirror-image copy of itself.  The copy efficiency and fidelity would have sucked, because the RNA was sitting in a soup full of organics and any number of other reactions (including reactions with other RNA molecules) could screw the whole thing up, but that isn't too important-- we've now got a large molecule that can replicate itself, at least under ideal conditions.  Step one.

Like I said, there was a lot of other crap floating around in the soup besides the sugars and amino acids that make up RNA.  Fatty acids, for example, probably would've also been present.  Fatty acids like to clump together into hollow pockets called vesicles, and it's not hard to imagine one of these vesicles eventually forming around one of the many RNA molecules floating around.  So now some of the RNA chains are isolated from the environment by a membrane.  Usefully, a fatty-acid membrane would have been impermeable to big RNA molecules (to prevent them from reacting with one another and essentially making a mess of their stored information) but easily permeable to the smaller amino acids and nucleotides needed for the RNA-replication reaction.  So by surrounding some RNA molecules with a fatty membrane, we've created a situation where some RNA can copy itself much more successfully than the membrane-less stuff.  So in other words, some RNA is now much better at transferring its information to its "children" than others, giving us a very primitive form of selection pressure.  Step two.  As a bonus, we've also created the first, very primitive, cell-like structure, with a membrane surrounding and protecting information-bearing macromolecules. 

The ancestor of all life on earth relaxes at home in the prebiotic slime.  The facial structure is somewhat conjectural.

Step three (possibility for occasional copying errors) pretty much takes care of itself, thanks to the inherent instability of RNA.  While the cell membrane protects the RNA well enough to ensure that most of its information survives the replication reaction, the whole thing is pretty much a self-catalyzed crapshoot; at some point some weird isomer of an amino acid is going to bind to the wrong place on the chain, or something.  What's crucial is that most of the information can still be transferred successfully, thanks to the membrane, but the system is still imperfect enough to spit out the odd error.

Mutation capability was a necessary component of the first protocells. 

Now that we've got everything we need for natural selection to take its course, we're off to the races.  The fact that the natural selection is occurring on molecules as opposed to anything that could even loosely be called "alive" is irrelevant; selection pressure is a purely statistical process and as such doesn't care whether it's screwing around with giraffe necks or the ordering of base pairs in an RNA molecule.  Natural selection in this case would favor moving toward better and better replication mechanisms, because more accurate replication would allow the RNA to make more accurate "children," so it's not too hard to picture the first simple, DNA-based prokaryotic cells eventually turning up after a few million years or so of refinement. 

While it's widely accepted that RNA was the original information-transferring molecule, it's entirely possible that it was preceded by some other, even more primitive nucleic acid.  We can't do a whole lot beyond educated guesses in that department, but people have done lots of interesting experimental work attempting to replicate probiotic-soup conditions and actually demonstrate a lot of this stuff.

So not only are we descended from monkeys, if you go back far enough we're probably descended from an unstable polymer sitting in a bubble of fat.  Can't imagine that's going to make the Jesus types very happy, but at least now I've got a good answer for the inevitable smug "well then where did DNA come from?" question whenever I'm dumb enough to actually try to argue with these people. 

Following my First Rule of Doing Science (it's way easier to find someone who knows a thing than it is to learn the thing yourself) I called in a ringer on this one.  He explained the gist of it to me and then pointed me to this article on the origin of life, which is an incredibly detailed (and well-cited) expansion of everything in this post.  It's entirely worth a read, and even having an at-best-passing knowledge of genetics and biology I was able to mostly understand it without having to type too many words into Wikipedia.


  1. I am glad you admitted that you are not an expert in Biology or Genetics. Since you are very interested in how this stuff works, you may want to read a few books from Francis Collins. I think his books will help you clean-up some of your arguments. Happy reading.

  2. Good day! I can see that you deeply get the sense of what you are writing about over here. Do you own an education that is linked with the topic of this post? Waiting forward to hear from you.