Life: 4 billion to 600 million years ago

While we don’t know many of the details of how life emerged, the latest theories connect a few more dots than we could before. Deep-sea hydrothermal vents 1 may have provided at least these four necessary precursors for early life to arise around four billion years ago:

(a) a way for hydrogen to react directly with carbon dioxide to create organic compounds (called carbon fixation),

(b) an electrochemical gradient to power biochemical reactions that led to ATP (adenine triphosphate) as the store of energy for biochemical reactions,

(c) formation of the “RNA world” within iron-sulfur bubbles, in which RNA could replicate itself and catalyze reactions,

(d) the chance enclosure of these bubbles within lipid bubbles, and the preferential selection of proteins that would increase the integrity of these outer bubbles, which eventually led to the first cells

This scenario is at least a plausible way for the precursors of life to congregate in one place and have opportunities for feedback loops to develop which could start to capture function and then ratchet it up. Many steps are missing here, and much of the early feedback probably depended more on chance than on mechanisms that actually capture and leverage it as information. Alexander Rich first proposed the concept of the RNA world in 1962 because RNA can both store information and catalyze reactions, and thus do both the tasks that DNA and proteins later specialized at. But whatever the exact order was, let’s just assume that in the first few hundred million years life arose.

(e) expansion of biochemical processes, including organized cell division, the use of proteins and DNA,

(f) the last universal common ancestor, or LUCA, about 3.5 billion years ago

Early life must have been very bad at even basic cell functions compared to modern forms, so the adaptive pressure in the early days must have mostly focused on improving the core mechanisms of metabolism, replication, and adaptation. As life became more robust, it became less dependent on the vents and was gradually able to move away from them. Although we know that all living cells on earth must descend from a single common ancestor roughly 250 to 750 million years after life first arose, this does include viruses. While there are several theories of the origin of viruses, I believe all viral lines are remnants of pre-LUCA strategies that evolved before the LUCA line was firmly established.

The central mechanics of life on earth evolved during these early years. Although the central mandate of evolution is survival over time, we can roughly prioritize the set of component skills that needed to evolve to make it happen. As each of these skills improved over time, organisms that could do them better would squeeze out those that could not:

1. Metabolism is, of course, the fundamental function as life must be able to maintain itself. A source of energy was critical to this, which is why hydrothermal vents are such a likely starting point.

2. Reproduction was the next most critical function, as any kind of organism that could produce more like itself would quickly squeeze out those that could not. This is where RNA comes in. RNA is too complex to have been the first approach used to replicate functionality, but one can imagine a functional ratchet that used simpler but less effective molecules first.

3. Natural selection at the level of traits is the next most critical function needed because it would make possible the piecewise improvement of organisms. Bacteria developed a mechanism called conjugation that lets two bacterial cells connect and copy a piece of genetic material called a plasmid from one to the other. Most plasmids ensure that the recipient cell doesn’t already have a similar plasmid, which protects against counterproductive changes. There are so many bacteria that a good strategy for them is to try out everything and see what works.

4. Proactive gene creation. Directed mutation is currently a controversial theory, but I think it will turn out that nearly all genetic change is pretty carefully coordinated and that the mechanisms that make it possible evolved in these early years. I am talking about ways a cell can assemble new genes by combining snippets of DNA called transposable elements that are then put back into chromosomes where their functional effects could be inherited by daughter cells. If these changes are done in germ cells they will affect all future generations. If organisms were able to evolve ways to do this in the early years, they could have easily outcompeted other organisms. I think much of the genetic arms race in the beginning focused on better ways to direct change, not because the result of such tinkering was known in advance but because organisms that tinkered with their own DNA when under stress survived better in the long run. Such directed mutation capacities probably started out by directly impacting the next generation so that they could be selected for right away, but over time were refined into strategies that could take many generations to produce new genes or even be held in reserve indefinitely until environment stress indicated that change was needed.2

The next big step was:

(g) the arrival of eukaryotes

Eukaryotes are now widely thought to have arisen by symbiogenesis, which is the absorption of certain single-cell creatures by others that resulted in one living inside the other permanently. Two organelles common to all eukaryotes have double-membraned organelles, which would be expected to occur if one membrane originated from the cell membrane of the endosymbiont while the other originated in the host vesicle which enclosed it.3 The first is the cell nucleus and the other is the mitochondrion. Algae and plants also contain plastids that also have double-membranes. Mitochondria and plastids reproduce with their own DNA, while cell nuclei seem to have become the repository for the host DNA. While eukaryotes need these organelles, their key evolutionary enhancement was sexual reproduction, which combines genes from two parents to create a new combination of genes in every offspring. Sexual reproduction is a nearly universal feature of eukaryotic organisms4 and the basic mechanisms are believed to have been fully established in the last eukaryotic common ancestor (LECA) about 2.2 billion years ago. In the short term, sex has a high cost but few benefits. However, in the long term it provides enough advantages that eukaryotes almost always use it. Asexual reproduction, which is used by prokaryotes (non-eukaryotes, including the bacteria and archaea) and by somatic (non-sex) cells of eukaryotes, is done by a cell division process called mitosis. During mitosis, a double strand of DNA is separated and each single strand is then used as a template to create two new double strands. When the cell divides into two, each daughter cell ends up with one set of DNA. Sexual reproduction uses a modified cell division process called meiosis and a cell fusion process called fertilization. Cells that undergo meiosis contain a complete set of genes from each of two parents. They first replicate the DNA, making four sets of DNA in all, and then randomly shuffle genes between parent strands in a process called crossing over. The cell then divides twice to make four gametes each with a unique combination of parental genes. Gametes from different parents then fuse during fertilization to create a new organism with a complete set of genes from each of its two parents, where each set is a random mixture from each parents’ parents.

Sexual reproduction is clearly a much more complex and seemingly unlikely process compared to asexual reproduction, but I will show why sex is probably a necessary development in the functional ratchet of life. The underlying reason for sex is that it facilitates points 3 and 4 above, namely natural selection at the level of traits and proactive gene creation. Because mechanisms evolved to do both 3 and 4 well, prokaryotes evolved in just two billion years instead of two trillion or quadrillion. Of course, I can only guess about time frames this large, but in my estimation evolution would have made almost no progress at all without refining these two mechanisms, so any organisms that could improve on them would have a huge advantage over those that did them less well. We know that conjugation is not the only mechanism prokaryotes use to transfer genetic material between; all such mechanisms outside of sexual reproduction are called horizontal gene transfer (HGT), and also include transformation and transduction, the latter of which is the incorporation of DNA from viruses. Any mechanism that can share genetic information at the gene or function level to other organisms creates opportunities for new combinations of genes to compete, which makes it possible for individual advantageous functions to spread preferentially to less capable ones. HGT has been sufficient for the evolution of two large groups of single-celled organisms, bacteria and archaea, and so is no doubt deployed in many strategic ways we can still only guess at, but the outcome is fundamentally pretty haphazard, which makes it inadequate to support multicellular life. On the one hand, it allows many new genetic combinations to be tried at a fairly low cost since the number of single-cell organisms is very high. But on the other hand, it lacks many mathematical advantages that sex brings to the table. I will assume “that the protoeukaryote → LECA era featured numerous sexual experiments, most of which failed but some of which were incorporated, integrated, and modified,”5 and that consequently a great many intermediate forms before LECA formed are no longer extant to give us insight into the incremental stages of evolution.6

What benefits does sex provide that led to its evolution? John Maynard Smith famously pointed out that in a male-female sexual population, a mutation causing asexual reproduction (i.e. parthenogenesis, which does naturally arise sometimes allowing females to reproduce as clones without males) should rapidly spread because asexual reproduction has a “twofold” advantage since they no longer need males. It is true that when resources allow unlimited growth, asexual reproduction can thus spread faster, but this rarely happens. Usually, populations are constrained by resources to a roughly stable population. Achieving the fastest reproduction cycle is not the critical factor in long-term success in these situations, and it is actually rather irrelevant. In any case, eukaryotic populations probably could and would have evolved a way to switch between sexual and asexual reproduction depending on which is more beneficial at the time, and very few ever choose asexual. This strongly suggests that sexual reproduction nearly always confers more advantages than asexual reproduction. We are aware of a number of such advantages, but I think the critical ones are better solutions to my points 3 and 4 above. Sexual reproduction is set up to create an almost unlimited number of genomes with different combinations of genes, while all asexual reproduction can do is accumulate genes (although prokaryotic genomes stay pretty small, so they must also have ways of knocking genes out). And sex pits each trait against its direct competitors so that natural selection can operate on each independently. Beneficial traits can spread through a population “surgically” knocking out less effective alleles, something asexual reproduction can’t do. Sex gives a species vastly more capacity to adapt to changing environments because variants of every gene can remain in the gene pool waiting to spread when conditions make them more desirable.7 Asexual creatures can’t keep genes around for long that aren’t useful right now, because they can’t generate new combinations. Horizontal gene transfer is apparently sufficient to allow prokaryotes to adapt, but obligate parthenogenesis in multicellular species leaves them with essentially no prospects for further adaptation and so represents a dead end. This includes about 80 species of unisex reptiles, amphibians, and fishes. All major vertebrate groups except mammals have species that can sometimes reproduce parthenogenetically.8 We can conclude that Maynard Smith was right that asexual reproduction provides a “quick win”, but because it is a poor long-term strategy its use is limited in multicellular life. Overall, I would estimate that eukaryotes are roughly 10 to 100 times “better” at evolution than prokaryotes, mostly because of sex, but their improved technologies really start to shine in multicellular organisms, because their ability to pinpoint the focus of natural selection allows complex organisms to arise.

(h) complex multicellularity, meaning organisms with specialized cell types.

Multicellular life has arisen independently dozens of times, starting about 1 billion years ago, and even some prokaryotes have achieved it, but only six independently achieved complex multicellularity: animals, two kinds of fungi, green algae (including land plants), red algae, and brown algae. The relatively new science of evo-devo (evolutionary development) is focused largely on cell differentiation in complex multicellular (eukaryotic) organisms. The way that the cells of the body achieve such dramatically different forms, simplistically, is by first dividing and then turning on regulatory genes that usually then stay on permanently. Regulatory genes don’t code for proteins, but they do determine what other regulatory genes will do and ultimately what proteins will be transcribed. Consequently, as an embryo grows, each area can become specialized to perform specific tasks based on what proteins the cell produces. The most dramatic power of this process is the ease with which radial or bilateral symmetry can be triggered. Most animals (the bilateria) have near perfect bilateral symmetry because the same regulatory strategy is deployed on each side, which means that so long as growth conditions are maintained equally on both sides, a perfect (but reversed) “clone” will form on each side. Evo-devo has revealed that the eyes of insects, vertebrates, and cephalopods (and probably all bilateral animals) evolved from the same common ancestor, contrary to earlier theory. Homeoboxes are parts of regulator genes shared widely across eukaryotic species that regulate what organs develop where. As evo-devo uncovers the functions of regulatory genes, the new science of genomics is mathematically proving the specific evolutionary origins of every gene. Knowing when it started to be used and roughly what it does will go a long way to building a comprehensive understanding of development.

Before I move on, I should note that all complex multicellular eukaryotes live symbiotically with countless single-cell bacteria, archaea, fungi, and protists, and also with viruses, which don’t have cell membranes at all. Evolution has built on its successes in surprisingly deep ways which we are only beginning to appreciate through scientific models.

  1. Nick Lane, “The Cradle of Life“, The New Scientist, 17 October 2009
  2. Adi Livnat, Interaction-based evolution: how natural selection and nonrandom mutation work together, Biol Direct. 2013; 8: 24
  3. Hartman H, The origin of the eukaryotic cell, 1984, Speculations Sci Technol. 1984;7(2):77-81
  4. Ursula Goodenough and Joseph Heitman, Origins of Eukaryotic Sexual Reproduction, Cold Spring Harbor Perspectives in Biology
  5. Ursula Goodenough and Joseph Heitman, Origins of Eukaryotic Sexual Reproduction, Cold Spring Harbor Perspectives in Biology
  6. Just as viruses are the only remnants of the pre-LUCA era, prokaryotes are the only remnants of the pre-LECA era, but both eras must have had a staggering amount of diversity and development now lost to us.
  7. Jef Akst, “Why Sex Evolved“, The Scientist, October 13, 2010
  8. Switch from sexual to parthenogenetic reproduction in a zebra shark

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