How Early Cellular Life Evolved

EDIT NOTE: Added some more information from another post of mine.

As I think of ways progression in Thrive can work, I realize how important background scientific information is for creating game design ideas. Of course, science helps Thrive be as realistic as can be, but at the same time, it can help Thrive be as fun as it can be. Probably the most important question that needs to be asked to create solid concepts around how we progress through various stages is why. Why was this specific adaptation an advantage? Why would the player want to progress? Why did life evolve a certain way?

And those are tough questions because life is really good at being simple. Movement, multicellular life, and eukaryotes are all really cool, but prokaryotes are incredibly successful – much more successful than eukaryotes. They need less energy, they reproduce even faster, they don’t need as many complex systems; the list goes on and on regarding the benefits of being a unicellular, asexual bacterium. Why are we here, and why have we become so complex? Those questions will undoubtedly be asked in Thrive, so it helps to know our stuff when thinking about game design.

One source of information I’ve really appreciated is “The Vital Question” by Nick Lane, which focuses heavily on the energy constraints of early evolutionary history, how those constraints were broken, and why certain complex traits, like multicellularity, the nucleus, and sexual reproduction evolved. It’s difficult to read at some points as a reader who’s good not-great with biology and chemistry, but I highly recommend it.

I noticed bits and pieces of information scattered across this forum regarding why things evolved the way they did, but nothing very cohesive and in depth. This book really expanded my knowledge, so I wanted to share this with the forum. Here’s some cool things I learned, and a general evolutionary path of life on Earth I wanted to share that can be useful for conceptualizing the way Thrive should be. It’s long, and might take multiple stops to fully digest.

Life likely evolved early on Earth (4.2 – 3.8 billion years ago) on a planet very different from our own. The creation of the Moon through a planetary collision, as well as continuous collisions from rocky material, likely meant that the very early ocean was incredibly warm. Life was likely largely thermophilic, having formed near alkaline vents and living in a heated ocean. However, the oceans cooled off rather quickly – otherwise, a lot of the water on Earth would have evaporated and runoff from our primitive atmosphere – allowing different forms of metabolism to form by around 3.7 bya.

Once temperatures cooled off, it is generally believed that sulphuric-metabolism evolved first and then anoxygenic photosynthesis followed, but we aren’t 100% sure. Regardless, anoxygenic photosynthesis evolved rather early in life, around 3.6ish bya, and much of the carbon cycle was rather well-developed by then. Rubisco, the iconic photosynthesis enzyme crucial for oxygenic photosynthesis, probably evolved in response to life’s inherent adversity to oxygen; perhaps rubisco served as a method for cells to get rid of oxygen rapidly, or perhaps rubisco was evolved in response to toxin warfare amongst bacteria from another cell which utilized oxygen-based poison. Rubisco allowed microbes to colonize shallower and less chemically-populated areas – before then, microbial communities were probably limited to specialists evolved to survive around various chemolithotrophic processes, such as sulphur or iron. The arrival of cyanobacteria and their oxygenic photosynthesis likely meant the rapid proliferation of cyanobacteria and a huge shift in ecological dynamics as they oxygenated local areas, although it would be a long while before enough oxygen is created to render the entire atmosphere aerobic. So pretty soon after life first evolved, photosynthesis, the carbon cycle, and the sulphur cycle could have been in place.

Another important biogeochemical process to bring up is the Nitrogen cycle, which evolved in multiple steps in response to the available amount of Nitrogen on Earth. Nitrogen is Earth’s most abundant gas and is endlessly important for life in the creation of proteins, but life cannot easily utilize atmospheric Nitrogen (N2); most lifeforms depend on breaking more accessible forms of Nitrogen, such as ammonia, nitrate, and nitrite, to meet their needs. There was a decent supply of accessible nitrogen in the ecosystems of natural Earth from lightning strikes, impacts, and other forms of chemical processes in those forms, with cells preferring ammonia due to how easy it is to breakdown – once this ammonia dwindled as life spread however, innovation needed to happen. Ammonification developed, which essentially is what decomposers do – break down organic (dead) material to create ammonia, and so did the reduction of nitrate and nitrite. The next step of the nitrogen cycle to evolve was likely denitrification, which essentially is utilizing nitrite and nitrate to generate ATP with Nitrogen (N2) as a waste product (not as efficiently as aerobic respiration). Although one form of bacteria is able to denitrify aerobically, the enzyme responsible for denitrification is incredibly sensitive to oxygen, meaning the process can be thought of as strictly anaerobic. Finally, nitrogen fixation, which is the ability of organisms to directly use N2 to create ammonia, evolved. Nitrogen fixation is also heavily sensitive to oxygen, but cyanobacteria, and another bacteria symbiotically attached to plants, have evolved the capability to perform fixation in aerobic environments. The final stage of the nitrogen cycle to evolve is nitrification, which essentially is autotropism based on nitrogen; being aerobic, it likely showed up after the arrival of oxygenic photosynthesis.

Aerobic respiration also evolved rather quickly after the arrival of cyanobacteria; in fact, oxygenic photosynthesis and aerobic processes appear to have emerged in almost the same geological instant. Again, the oxygenation of the entire atmosphere would be a while away from the emergence of oxygenic photosynthesis – atmospheric oxygen concentration was around 3% until the Cambrian Explosion, when it jumped to around 13% before rising through fluctuations to modern levels. However, localized oxygen contents, such as near the cyanobacteria dominated ocean surface layers, were high enough to support a healthy population of aerobes. Obligate anaerobes, such as red sulphur bacteria, were relegated to the open and lower levels of the oceans. The oxygenation of the entire ocean likely occurred around 600 million years ago.

Individual groups of prokaryotes are very diverse. In fact, closely related prokaryote species can oftentimes have as much metabolic diversity (different feeding strategies) than the entire eukaryotic domain. This is largely because of lateral gene transfer. We’ve become accustomed to evolution being a really linear reproduction-based method of selection with traits popping up very gradually from shared ancestral traits, but lateral gene transfer was (and still is) really, really important for prokaryotes. Prokaryotes would literarily pick up genetic material and incorporate it into their genome, rapidly shifting metabolic pathways to become accustomed to new environments.

The prokaryotic period of evolutionary history was also generally a lot more “peaceful”. We have grown accustomed to things like “predator” and “prey”, competition, and other similar selective pressures, but for the first two billion years of life, there wasn’t too much predation going on. Phagocytosis as an active predation mechanism, while in some archaea, isn’t either immensely ubiquitous or too ancient, and is generally thought to be relegated to eukaryotes.

Instead of predation, the main form of an “arms race” with prokaryotes revolved around minimizing reproduction costs. Because prokaryotes are so small, they reproduce very quickly, seeking to hog as much of an energy niche as they can. As such, niches were saturated with bacteria, and any minimization of reproduction rates was a deciding factor in which population would come out on top. For example, the more successful photosynthesizing cyanobacteria weren’t necessarily the one with the best photosynthetic “hardware”, but the ones that had decent enough hardware to remain afloat and a streamlined amount of genetic material so that reproduction remains fast. And the most successful bacteria were the ones who found the optimal medium; efficient, but not complex enough to bloat genetic material; and simple, but not simple enough to be obsolete. Contain enough genetic material to be able to rapidly uptake genetic material and shift metabolic strategy, but not enough to have unnecessary functions wasting energy and bloating reproduction.

So with lateral gene transfer offering prokaryotes the ability to rapidly pivot adaptations towards new environmental conditions, and with reproduction rates being the name of the game, there wasn’t really any pressure for complexity to arise. Although similar prokaryotic species can be more metabolically diverse than the entire eukaryotic domain, morphologically, prokaryotes have basically remained the same for three billion years of evolutionary history. For three billion years, prokaryotes were practically all asexual, had no organelles, mostly had cell walls, and otherwise, were membranes containing “simple” metabolic pathways. Until for some reason a billion years ago, one prokaryote engulfed another, and then the complexity of evolution was unleashed. Why did that moment happen? Why were prokaryote species “left behind” by eukaryotes, and why couldn’t they ever catch up in rate of evolution, size, and complexity?

We’ve been talking a lot about the benefits of being prokaryotic, which are profound: there’s a reason they immensely outnumber eukaryotes. One detriment however is that prokaryotes cannot be very big. Previously mentioned factors detailing how minimizing genetic material and reproduction costs sere as a very lucrative incentive for prokaryotes to remain small, but at the same time, it is energetically undesirable for a prokaryote to become bigger.

Size for a cell has the benefit of an increased surface area, meaning more space for reactions with a cell’s environment to occur. Let’s say that you multiple the surface area of a cell by 10. ATP generation potential thus increases by 10. But ATP generation isn’t as simple as having a membrane; you need 10 times the amount of channels maintained in the membrane to maintain equilibrium and generate ATP (which needs ATP), you need 10 times the amount of ribosomes needing 10 times the amount of ATP to create enough proteins for a larger cell, you need 10 times the amount of ATP to create enough lipids for 10 times the amount, etc. So yes, you get 10 times the amount of ATP generation. But at the same time, you get 10 times the amount of energy demands; and this doesn’t even mention the amount of volume you’ve taken on, which would need much more energy to maintain (volume increases much faster than surface area after a certain point). You end up with the same amount of ATP generated, but you have much more genetic material to copy. Why would a prokaryote want that?

Eukaryotes escaped this problem through endosymbiosis with mitochondria. Certain cells evolved the capacity to live within a cell’s cytoplasm, and that resulted in an insane amount of energy generation. Because the inside of a cell is a stable environment, the genome of those cells could be incredibly simple – there isn’t a need to protect yourself against a harsh environment and maintaining equilibrium is much easier, so it becomes much easier to streamline genetic material for faster replication. But another benefit to having a reduced genome is the amount of ATP saved. Nick Lane states that losing 200 genes means reducing maintenance costs by half-a-billion ATP. Each gene codes a protein made up of an average of 250 peptides, and each peptide bond needs about 5 ATP to be formed, meaning about 1,250 ATP is needed per protein. There is an average of 2000 copies of a random protein in a bacteria, meaning about 2,500,000 ATP. If each gene costs about 2,500,000 ATP, 200 genes results in 500,000,000 ATP saved. And around 200 genes are needed to code for the prokaryotic cell wall – the first item to be discarded by a cell within another cell. Without needing to worry about the environment, and with all this loosened amount of energy, these cells became incredibly powerful generators of ATP.

As this relationship became more established, exchanges of genetic material occurred which benefited both cells. The mitochondria had a vested interest in the survival of host cells, so the sharing of energy made sense. And “in return”, mitochondria could transfer and streamline more of its genetic material, such as that necessary for reproduction, into the genome of the host. In this exchange, certain parts of genetic material overlapped – the host cell didn’t need as much genome focused on generating ATP for example, and the mitochondria dumped even more genomes unnecessary in the safety of cytoplasm. All this extra unused genetic material, although useless at first, could be reorganized and recoded in a way by the host as seen fit – imagine lateral gene transfer, except magnified intensely. Previously, this would mean bad things for the parent prokaryote – more genome means more information to copy, meaning more of a reproduction cost. However, the extra generation potential of mitochondria – the addition of an entire cell’s worth of energy generation without any of the costs attached with maintenance – meant much, much more ATP, breaking the energy constraints early prokaryotes faced. And with much less of an energy constraint, barriers to size and complexity were intensely mitigated.

Some problems emerged out of this otherwise heavenly endosymbiosis. Genetic parasites – DNA that requires and “seeks” a host to reproduce, such as viruses – have always been a problem for prokaryotes. Added genetic material means more energy and a slower reproduction speed, which meant bad news for life at this point. This new endosymbiont escaped this energy/reproduction problem with the added ATP generation of mitochondria, but when these genetic parasites would die within their more long-lived host, they would leave genetic material that didn’t do anything cluttered in the host cell’s genome – modern day introns – that could obviously lead to complications. Today, eukaryotes have advanced mechanisms to deal with introns that can lead to increase genetic variability – but back then, this was rather troublesome for our proto-eukaryotes, and even now, those mechanisms might not operate fast enough to catch all junk DNA. And with the exchange of genetic material between mitochondria and the host genome, the opportunity for genetic parasites to emerge was heightened.

Fortunately, there was also a solution present with endosymbiosis. In this transfer between the alien endosymbiont and the host cell, the endosymbiont’s genetic material coding for the production of lipid membranes was likely exchanged– information to create a solid membrane was not needed in a very safe and stable cytoplasmic environment. This probably meant that at some point, the host cell might have created lipids inherited from the mitochondria in the middle of the cell. While this obviously could lead to many complications, in fluids, lipids naturally form hollow spheres (the origin of life likely involved the formation of lipid spheres first and then those sphere’s acquisition of genetic material). For some lucky host cells, this lipid membrane would go on to enclose genetic material. Now, there was a natural barrier between viruses and other infectious genetic material, blocking DNA without specific clearance from hijacking a ribosome and creating unneeded proteins. The birth of the nucleus.

The development of sexual reproduction quickly followed. With so much genetic material and so much exchange between the endosymbiont and host cells, mutation rates rapidly increased. This can be a good thing: mutation means more variance, and more variance means a more robust population. But for asexual reproduction, rapid and uncontrolled mutation can be rather deadly. The more mutation there is, the more negative mutations there will be. As many generations reproduce, those negative mutations build up, leading to a degenerating genome and continuously lowering fitness. However, even a positive mutation in a rapidly mutating asexual population can be bad news. Asexual reproduction copies the entire genome, so individual mutations or genes aren’t selectively pressured – the entire genome is. So a genome with a positive mutation that spreads across the population might have obscured the 5 negative mutations coming along with this new genome – essentially a genetic Trojan Horse. Extinction might soon follow should the environment shift, a new disease pop up, or other new conditions arise which severely punish those bad genes. What is worse for our newly-evolved eukaryote is the immense size of its genome – the more DNA there is, the more chance there is for mutation.

Sexual reproduction is beneficial in that chromosomes might differ in structure and the way those chromosomes combine with another chromosome. With asexual reproduction, the entire genome is read the same way every time, so the order of genes stays the same – remember, the entire genome is judged, not specific genes. With sexual reproduction, two genomes from two individuals randomly exchange small chunks of DNA, resulting in a different expression of certain traits in every individual and increased variance (genomes across individuals of the same species have the same genes, but may have a different sequence of genes). This essentially allows specific genes to be judged instead of the entire genome. Certain lucky individual cells inherit more good mutations than bad. Those cells do well and reproduce, passing on an overly better genome to the next generation. Certain unlucky individual cells inherit more bad mutations than good. Those cells do bad and die before reproduction, halting a more negative genome from passing onwards. Throughout time, the population trends towards a better genome, as the more favorable genome combination-offspring survive more than the negative genome combination-offspring.

Selective pressure for better offspring increases. Escaping from the continuity of asexual reproduction, eukaryotes more quickly build up positive genes and discard negative ones. Another endosymbiont – this one with thylakoids – catches on with a specific group of eukaryotes. Cells bond. Tissues differentiate. Structure and symmetry form. Limbs form. Roots grow. Animals emerge. Fungi emerge. They reach the surface. They fly, swim, and stand upright. And here we are.

Any questions? If a specific piece of the post doesn’t make too much sense, I can look for more detail.