Origins of Life

Origins of Life August 29, 2017

My old blogging compadre, Smilodon’s Retreat, recently chipped in on some abiogenesis chat on a few threads I posted. He has kindly let me repost an old piece of his that should have some relevance. It can be found in original for here at his home at SIN. It’s a few years old but still has every relevance. Over to him:

One my areas of interest is the Origin of Life.  That’s caps for a reason.  What was the first living thing like?  How did it arise?  What does it mean to be alive?

Those are all fascinating questions and not easily answerable.  We will never know what the first living thing was like.  That information is buried in deep, deep time and wouldn’t fossilize anyway.  But we can know whether it is possible for something that is alive to come from something that is not alive.  If it’s possible, then many of the creationist arguments about OOL are moot.

What few people realize is how much effort is being put into OOL research.  Starting with Stanley Miller and Harold Urey in 1952, OOL research has grown significantly.  In those 60 years since the first Miller-Urey experiment (which is now being copied in high school biology classes), there hasn’t been a single result that shows any chemical reaction that is needed for OOL cannot happen.

All it would take is one experiment.  One bit of chemistry to show that, most definitely, it is physically impossible for x and y to combine in this way, which means that natural origins of life are impossible.  In 60 years, that hasn’t happened.  In fact, there are often multiple pathways to the various compounds.

Let me provide a brief overview of some of the research.  First, we have to define life… but I’m not going to.  That’s a hugely complex area and the blood tends to get deep when philosophers and scientists start trying to define life.  Like porn, we know it when we see… or at least we pretend that we do.  I disagree, but that’s not my point today.

First, we know that organic compounds are common.  When most people think of organic compounds, they think of things that had to come from life.  But that’s not the case.  There is a large variety of places where organic compounds exist that we are confident that they didn’t come from living things. For example  Titan,  nebula, and meteorites.  So I hope that there are no concerns with the fact of organic compounds forming.  In fact, the atmosphere and conditions on Titan have been shown to be able to form all five nucleotide bases as well as amino acids.

Now, creationists will always complain about odds.  What are the odds of primordial compounds coming together and forming a human being… or even a single protein or DNA strand of that human being.  Fortunately, we’re fairly confident that the first living thing on Earth wasn’t a live human being… in spite of what part of one particular book of myths claim.

Part of the problem with Origins of Life hypotheses is that they are complex.  There has to be a way to store, use, and copy information.  There has to be a way to extract, store, and use energy.  There has to be a container.  These are not little problems.  And the creationists point to these problems.

But what if it was simpler than we think?  What if the method that stores information is also the method that extracts energy?  That’s the whole premise of the RNA-World hypothesis.  You see, RNA can store information, but it can also act as a catalyst.  Further, it is capable of self-reproduction.

Here’s an interesting paper that talks about how complex the first RNA had to be that was capable of catalyzing a metabolic reaction. So, how big does the simplest RNA have to be?  5 nucleotides.  That’s all.

Given 4 possible nucleotides, what are the odds that random assembly of 5 of them will result in an RNA that has a useful function?  Pretty darn good actually.  You see, the active site in that 5-nucleotide RNA is actually only 3-nucleotides, the other two can be pretty much anything.

Further, there isn’t just one 5-nucleotide sequence that has a useful function.  There may be thousands of them.  From the paper:

The ultimate importance of these observations may lie partly in the unknown number of other reactions that can be accelerated by comparably small RNAs. This is because for each such minuscule RNA reaction, there is a prima facie case that it would become accessible even after the most primitive ribonucleotide polymerization.

To see this, consider that, to pick every possible RNA pentamer sequence from arbitrary pentamers (with probability 0.9975), one needs only accumulate 4.1 × 10−18 gm of RNA. To possess every tetramer (with probability 0.9975) from a pool of  arbitrary tetramers, one would need 3.4 × 10−18 gm RNA. In a real polymerization, one would have a distribution of lengths; nonetheless, with only attograms of total RNA of distributed short lengths from some geochemical source, one would have not only our ribozyme, but every activity of comparable size.

But that all presupposes that nucleotides can self-assemble into strands of RNA.  So, can RNA self-assemble?  The answer, as shown by Matthew W. Powner, Beatrice Gerland & John D. Sutherland, is simply… yes.

The problem is that ribose (the sugar that makes up the backbone of DNA and RNA) is difficult to form.  Even worse, is that it is nearly impossible to attach a purine nucleotide to a ribose and it is impossible to attach a pyrimidine nucleotide to a ribose.

Well, that should be the end of it.  Incontrovertible proof that RNA can’t self-assemble… except the authors found another method.  An alternate pathway, instead of the obvious one.  Another chemical pathway in which inorganic phosphate acts as a catalyst. Further, the use of inorganic phosphate acts as a buffer to keep the pH in the appropriate range for RNAs to form.

Our findings suggest that the prebiotic synthesis of activated pyrimidine nucleotides should be viewed as predisposed. This predisposition would have allowed the synthesis to operate on the early Earth under geochemical conditions suitable for the assembly sequence.

Well, now we have the pieces, those nucleotides with phosphate and sugar backbones that can become RNA strands.  But can they self-assemble?  The answer is yes, in at least two ways.

One way is by using clay as an assembly substrate.  This has been known since the early 90s.  The second happens, amazingly, in just the way Darwin described, before we even knew about atoms and biochemistry.  The assembly of long chain RNAs can happen in nothing more than a warm little pond.

They tested cyclic nucleotides in a variety of conditions and found that RNA strands spontaneously formed in water that was warm (40°C to 90°C).  Further, these RNAs formed quickly.  An eleven nucleotide strand formed in less than a minute.  After 100 hours, RNA strands of over 100 nucleotides were formed.

Recall that it only takes 5 nucleotides to form useful ribozymes.

So far there are no barriers to get from raw organic compounds to RNA strands 10s of nucleotides long.  Now for the critical step.  Can RNAs self-reproduce?

This paper wasn’t written to show how life on this Earth appeared, but merely to show that it is possible for RNAs to self-reproduce.  That’s all.  So, in one respect, it’s not that useful.  But in another aspect, it shows that it can happen.  Remember, it only had to happen once.

Dr. Joyce was working on self-replicators.  The added bonus is that this shows it’s possible.  My latest information from Dr. Joyce was that they had a library of over 65,000 RNA replicators.  The purpose is to demonstrate the development of novel functions using only evolution.  I need to get back in touch with him and see what’s new in his lab.

So that’s just the stuff I’ve delved deeply into.  But is there more?

Oh, heck yeah. That link is to the abstract list of the International Conference on the Origin of Life, 2008, held in Florence Italy.

There were 310 presentations, with 260 posters, covering things from planetary system formation to gas-phase prebiotic chemistry in our solar system.

And so far, none of them have concluded that it is impossible for living systems to form from non-living systems.

One thing I often hear from creationists is, “But it hasn’t been done in the lab”.  So far as I know, no one is actively trying to start from a Miller-Urey type experiment and letting it run until an amoeba crawls out of the tank.  What would be the point?  Besides the fact that it would take decades…

But the Earth had time.  The best estimate is that the Earth is 4.5 billion years old.  Chemistry is fast.  Once you get nucleotides, then it can take minutes to form long chain RNAs.  If even one of them is a catalyst, then it can help other long chains form.  Soon it may be that you get a self-replicator… or even a general replicator.  It could happen in days or centuries.


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