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On the Origin of Life
by Tom Veatch
I'm no professional biochemist, but here's something very
interesting
which I haven't seen anyone explain before.(as of the early 2000's when I first wrote this). I think that the single, miraculous, random event that keyed L.I.F.E...is:
reverse transcriptase.Or, you might say, the random assembly of nucleotides comprising, suddenly, the RNA sequence from which RT is generated. The idea is that...
- 1) in a puddle of nucleotides, fats, and amino acids, all expectably present in the pre-life Earth environment, carrying out some natural level of protein synthesis weakly and slowly,
- 2) where the nucleotides in the puddle would combine in random sequences by the weak chemical bonding natural to them, (all expectable), these sequences being small RNAs and DNAs, and
- 3) where from those RNAs are generated proteins, using the amino acids and the driving energy of day/night cycling (all expectable), then
- 4) one of the RNA sequences generated was the random RNA which happens to be the one that codes for reverse transcriptase. This event (4) is the key, single, almost-but-not-actually-miraculous, random event in the creation of life according to this view. Then,
- 5) that RNA produced one or more reverse transcriptases using the protein synthesis going on in the puddle, and
- 6) the reverse transcriptase started doing its wonderful thing, which is generating a lot of DNAs from the nearby RNAs, and it's no miracle that that would include the DNA that its own RNA conceptually determines,
- 7) I have to wave my hands about the transcription of DNAs to RNAs, because now we have DNAs and need to get to the same RNA again, but once we get that, then
- 8) an extra copy of the RNA for reverse transcriptase appears having
been transcribed from that DNA. Presto, reproduction.
- 8A) Lots of copies of reverse transcriptase and its RNA and DNA can quite reasonably fall out of this without any miracle required, since it is right there in the soup next to its own RNA and can keep making lots of DNAs over and over. And so then
- 9) with reverse transcriptase floating about, converting randomly-generated RNAs into DNAs which themselves transcribe into RNAs, the soup now has a bunch of random RNA/DNA strings undergoing replication, along with a lot of replication engines and replication systems for the replication engine itself. So
- 10) then Darwin's logic applies: More replicatable stuff that randomly occurs, that happens to work better at being around for replication, and that therefore survives longer in the environment of replicating engines, will happen to get replicated more, and thus there will be a drift towards adaptive and useful parts, and to their combination in adaptive and useful ways, since those parts and combinations happen to be around longer and thus are present for replication more and therefore are replicated more often and therefore come to be more common.
Tom Veatch
P.S. Am I wrong? Please send your comments to me here.
2022 Update
Here are my notes from Professor Nick Lane's talk at the Royal Society of Biology East Midlands on "Energy and Matter at the origin of life" which says that a possible locus of this evolution was in undersea vents which are presently visible in a few certain places under the ocean. Apparently water goes deep into the rocks below, encountering "maphic" minerals like olivine, reacts to generate heat, alkaline fluids, and lots of hydrogen gas, and serpentinite rocks, the hydrogen and alkali fluids percolate back up and come out in what are called alkaline hydrothermal vents, different from the hot black smokers, these are warm, and they produce sponge-like precipitated mineral stones with small cavities and channels, which are themselves much like cells with a strong pH gradient across the walls, and with a lot of available life-like chemistry to use to create fatty acids and things like actual cell walls in which membrane chemistry can happen and membrane bioenergetics might evolve. Lots of H2 and CO2 as there was then, mildly acidic oceans, with inorganic pores containing alkali fluids surrounded by acidic fluids, rather like cells.Nick Lane reports that this subject was only taken seriously by chemists from the 1950's, how to make the nucleotide building blocks, etc. But much has changed in the last 10 years. To start early, Schrodinger, wrote What is Life, 1944, using words like "Codescript", thinking about life as encoded information, and entropy, and free energy.
Footnote: Lane is confused about entropy and life; Schrodinger got it right saying complex life sustains itself by sucking orderliness from the environment. Orderliness can be considered like sortedness, and when processes take a bunch of an input and make heat and other random movement, they are consuming that bunch, that bit of a sorted pile of everything, that orderliness, and turning it into randomness. Lane didn't seem to understand this. Perhaps because orderliness (the opposite of entropy) could mean different things, like more useable photons or more useable water molecules or more movement of anything or more measureable quark states being the same, and sometimes from one view order seems like disorder and disorder like order. All the atoms in a crystal might seem ordered, but their quark spin states might be discorrelated and thus quite disordered. From one perspective some gas in a chamber is perfectly ordered as it is all at the same temperature and pressure and the average velocity of the molecules is in a narrow range, but from another perspective any of them could be anywhere in the chamber and so they are fully disordered. Some such confusion like this might make biologists feel that Schrodinger was incomprehensible.Free energy is the energy available to carry out work, mainly in life, ATP available to be hydrolysed, a normal non-biological chemical process where the third phosphate pops off the ATP and becomes adenosine di-phosphate.
Proton gradients across membranes are also universal in life; they power life. A proton is an ionized hydrogen, H+, and in respiration, protons pass through the membrane through a membrane pump that hooks two of them up with two electrons and an Oxygen to create an H20. The membrane pump is called ATP synthase, and it rotates in a hole in the membrane, so there is a lot of pumping of protons to one side of the membrane. This being so complicated, science thought it couldn't be primordial but had to be evolved. Terrestrial ponds are the favorite site of many scientists, and they use that chemistry including Yellowstone volcanic pools, along with wet/dry cycling, to do the chemistry but it looks not very life like as regards pathways, substrates, etc. But what looks more like life, as we know it, is in the undersea vents.
We need metabolism, cells with cell walls, and the genetic information encoding. Read Christian deDuve: How do you go from protometabolism to metabolism? With biological catalysts. Then how did BCs with appropriate properties appear? By selection.
The chemical environment that would have favored the origins of biochemistry, is revealed by a tree of genomes (Bill Martin, 1999, Mosaic bacterial chromosomes...a tree of genomes, BioEssays 21:99-104), which had a few crossings of branches, like the eukaryotes got the stuff like nuclei and another branch got mitochondria injected into them so they couldn't have been primordial. A common ancestor of bacteria and archaea is necessary to account for many shared characteristics, a universal genetic code, ribosomes, transcription, translation, krebs cycle and membrane bioenergetics, while differing in striking aspects, such as the chemistry of the cell membrane and wall, different genes for glyolysis, even DNA replication genes are mostly divergent.
Continue from 20:00 of the talk.