In the Beginning

Well, no, not the beginning of everything, or even much of anything, in the context of our grand and glorious universe, but it was still a pretty important beginning as far as we are concerned, and that is the beginning of life on earth.

As you will no doubt not recall, in our last episode of this long-running series, I summarized the four essential components of life as we know it:

• A cell membrane consisting of a phospholipid bilayer. This serves to create a protected compartment in which the processes of life can take place unmolested.
  
• Information for making proteins encoded in DNA.
  
• A mechanism for making proteins using said information, built out of RNA.
  
• Proteins.

As I also said, once you have any chemical system that can catalyze its own replication, with the possibility of imperfect copying, Darwinian evolution can begin. By all indications, there were indeed a lot of complex organic molecules present in the primitive ocean, including all the essentials: phospholipids, amino acids (the building blocks of proteins) and nucleotides (the building blocks of DNA and RNA). (Viz the famous Stanley Miller experiment.) We know that life appeared within a very short time, by geological standards, after the bombardment of earth by debris from the formation of the solar system slowed down enough to allow the crust to cool and the oceans to form -- no more than 200 or 300 million years, and probably less.

Okay, so it must be easy to get life happening on a planet with the right conditions, no? Maybe so, but nobody has quite figured out how to do it yet. I say this with some trepidation because here is where the creationists love to pounce. "You can't figure out where life comes from, so God must have done it!" But of course, people used to attribute plagues, earthquakes, and volcanic eruptions to God, but now we have figured out why they happen, and God has nothing to do with it. (A conclusion which the faithful ought to welcome, since it would seem to salvage a good part of God's reputation, but for some reason most of them don't. Oh well.) So this is just one more thing we need to figure out.

The major difficulty is that you need to have all four of those components working together, but which came first? And how could it have come first, since they are dependent on each other? DNA can't be copied for reproduction, or read for protein synthesis, without proteins and RNA; proteins can't be manufactured without RNA, at least, and RNA doesn't get made without proteins and DNA. The cell membrane is also put together by proteins -- and, an important detail, is pierced by various proteins which act as gatekeepers, determining what gets in and out.

But maybe the cell membrane is the least problematic element. Specific control over what passed through the membrane may not have been necessary in the beginning. It's a great improvement, but could have come later. Phospholipids will form compartments spontaneously in solution. It is conceivable that a pre-biological chemical system that catalyzed the formation of lipid bilayers could have arisen spontaneously. It would tend to persist because it would be protected within its lipid bilayer bubble, but would "reproduce" when the bubbles did happen to burst due to wave action or other causes. If the fragments could go on to recruit lipids from the solution and form new bubbles for themselves, you would have a self-reproducing system and perhaps be on the road to life.

This isn't hard to imagine but nobody has come up with a working example yet. Another possibility is that life started in some other sort of compartment. One proposal concerns tiny holes in volcanic rock near hydrothermal vents in the deep ocean, and says that live may have evolved there for a while before some organism lucked onto the lipid bilayer trick and so freed itself from the rock.

Even so, you've got to figure out how the DNA-RNA-Protein complex could have arisen. DNA stores information to make proteins; proteins catalyze chemical reactions; RNA mediates between them. The problem of how this complex system could have been assembled originally seemed much more tractable after Sydney Altman and Thomas Cech discovered that RNA molecules could, in fact, catalyze chemical reactions, including excising pieces of themselves. Since RNA can store information in the same way DNA does, it appeared the problem was solved, and so-called RNA World hypothesis was born, as advocated here by Christian de Duve. Catalytic RNA molecules, called ribozymes, could have constituted the first self-replicating chemical systems. Once you have the RNA world going, it doesn't seem terribly difficult for the DNA and protein systems to develop around it, and for the repository of genetic information ultimately to shift to the more stable, and easier to replicate, double-stranded DNA. (Today, so-called retroviruses, including HIV, store genetic information as RNA, and copy it into DNA. So it's obviously possible!)

Alas, formidable difficulties remain. I'm 100 miles from being a specialist in the relevant chemistry, or any sort of chemistry, but those who know say that in the hypothesized pre-biotic environment, many factors would have conspired to terminate RNA chains before they could get up to critical size, and to destroy at least one of the essential nucleotides, among other problems.

The problem is sufficiently challenging that it has inspired many surprising theories. William Martin and Michael Russell believe that the earliest life was not based on organic chemistry at all, but on iron sulfide inside rock. And of course, most boggling to the mind is the panspermia hypothesis, which says that microbes pervade the galaxy and travel between stars as spores embedded in rock. Hence earth was seeded with life from space. This still doesn't answer the question of how life got started in the first place, of course, but it makes the range of possible places and conditions essentially unlimited. It also suggests that if people one day travel to other star systems, they will encounter DNA-based life, perhaps even prokaryotic cells a lot like our own.

You know what folks? I have no idea. And that's good, because it means there is a thrilling journey of discovery still ahead of us. And that is far more satisfying than reading and re-reading a musty old book by people who knew even less than we do.