Origin: Complex Designs in Evolution
In our last issue, I left you with a question: If the development trend of bacteria is to become simpler and if there is a mechanism of horizontal gene transfer
This brings us to the mitochondria.
Mitochondria originated approximately 2.1 billion years ago, while the earliest life on Earth appeared around 3.7 billion years ago. This means that the competitive survival strategy
Let's start from over two billion years ago.
Back then, life on Earth consisted only of bacteria and archaea, which are structures of simplicity but not simplified to the point of only retaining the function of replicating themselves. After all, they needed the ability to obtain nutrients. Otherwise, what would they eat?
So, what did they eat? Anything available, with the easiest option being food near hydrothermal vents at the bottom of the ocean. However, archaea a bit further from the vents faced a food shortage, with many inevitably starving to death. A type of archaea evolved a new structure that allowed them to consume a different kind of food — green light.
This is based on the "Purple Earth" hypothesis proposed in 2007 by American biologist Shiladitya DasSarma.
The hypothesis suggests that the first photoautotrophic organisms appeared on early Earth around 2.4 billion years ago, using retinal instead of the chlorophyll that dominates today. They absorbed green light because, in terms of energy distribution, green and yellow light have a higher energy ratio in sunlight. Once organisms could utilize light energy, green and yellow were likely the first spectra to be used.
As mentioned, these photoautotrophic units used retinal, a substance much simpler than chlorophyll. Retinal photosynthesis doesn't produce oxygen but generates water, sugar, and sulfur instead. Green light drives transmembrane proteins to push protons out, creating a waterfall effect that rushes back in to charge ATP, thus providing energy.
These ancient bacteria dominated the ocean's primary ecological niches
However, competition among these ancient bacteria was fierce. Those that couldn't float on the surface to consume green light, being pressed into lower layers, died off en masse.
Among them, a very few utilized porphyrin to absorb red and blue light. Porphyrin is a precursor of chlorophyll.
This hypothesis emerged partly because some scientists wondered why chlorophyll, despite its ability to absorb light energy, is tuned to two distinct wavelengths — long wavelengths for red and short wavelengths for blue and violet. Given that the most abundant energy in sunlight is in the green and yellow spectra, it seemed odd not to use the best available energy but to resort to what's left. Indeed, they were essentially consuming what others did not.
The photosynthesis led by porphyrin produced a potent metabolic by-product of that era — oxygen. On a primarily reducing Earth, oxygen was toxic to most life forms. Thus, the first generation of photoautotrophic bacteria, which had been dominant for hundreds of millions of years, was poisoned by oxygen.
With sunlight being an inexhaustible resource, oxygen gradually increased in the sea and even made its way into the air, oxidizing methane — a greenhouse gas far more potent than carbon dioxide. When methane was oxidized on a large scale, Earth's "blanket effect" weakened. From 2.4 billion to 2.1 billion years ago, over this lengthy 300 million years, Earth was a giant snowball, frozen from the poles to the equator, known as the "Huronian glaciation."
The oxygen produced by chlorophyll and the sudden drop in temperature nearly wiped out all life at the time. When Earth warmed up again, only a few aerobic bacteria survived. They continued the trend of simplification, merely transitioning from anaerobic to aerobic bacteria.
Perhaps due to this dramatic change in life forms, some aerobic bacteria lost the ability to produce cell walls in a mutation event. Luckily, they still had cell membranes to prevent internal spillage and managed to survive.
Actually, lacking a rigid cell wall was advantageous, allowing for flexible body shapes. When one such bacterium happened to indent itself into a pocket shape, and another ancient bacterium was at the indentation, it inadvertently ingested the latter. This ingested ancient bacterium didn't die within the host or kill its host but found some nutrients and oxygen in the host's "stomach," starting to produce ATP using the host's raw materials.
This roughly describes the process by which mitochondria appeared inside an ancient bacterium.
Today, one hypothesis is that this process began with a methanogen engulfing an α-proteobacterium, which then led to the emergence of e
ukaryotes.
What are eukaryotes and prokaryotes, and what are their differences and similarities? Many textbook entries require memorization, but the initial difference between the two was whether DNA was enclosed in an additional membrane. This extra membrane originated when a methanogen engulfed an α-proteobacterium, leading to horizontal DNA transfer.
A segment of the α-proteobacterium's DNA, responsible for cell membrane production, drifted from its DNA and inserted into the methanogen's DNA. While the methanogen's DNA also synthesized cell membranes, the proteins would drag this membrane to the correct location, the methanogen's outer shell. The newly inserted segment, although also producing cell membranes, got stuck in transportation, so the surplus α-proteobacterium cell membrane accumulated near the methanogen's DNA. Eventually, enough accumulation led to another layer of membrane around the methanogen's DNA, forming the precursor to the cell nucleus and giving rise to eukaryotes.
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Eukaryotes had a significant advantage
Firstly, they overcame energy limitations through a large number of mitochondria.
If an ancient bacterium could only produce ATP via its surface respiratory chain, its size would be limited. Doubling its diameter would quadruple its surface area and thus its energy production, as ATP is generated on the surface. However, its volume would increase eightfold. In other words, ATP production capability increased quadratically, while energy consumption increased cubically, making size growth unsustainable.
With mitochondria densely packed in three-dimensional space to generate energy, energy production could increase cubically with size, no longer constrained by quadratic growth.
This evolutionary step took a long time, or else the transforming bacterium itself would have used up all the generated energy, leaving little for the methanogen.
This lengthy evolution waited for the α-proteobacterium to streamline most of its redundant DNA, retaining only replication and ATP production functions. Thus, when replicating itself, the α-proteobacterium consumed minimal energy. Once energy supply was no longer an issue, eukaryotes embarked on the path of DNA length liberation.
Previously, we discussed the rationale behind bacteria's evolution towards simplification: the need to reproduce quickly and the insurance of horizontal gene transfer. Now, a second successful model emerged: having abundant energy, allowing for complexity. This is the eukaryotic model, and both you, the listener, and I, the recorder, are victors evolved along this path.
Although I discussed the definition of life in our first issue, under which most biologists do not consider viruses to be living organisms, viruses are inseparable from life and exemplify evolution at every turn.
There are three main hypotheses on the origin of viruses: the regressive (degeneracy) hypothesis, the DNA mutation hypothesis, and the abiotic (spontaneous generation) hypothesis. Of course, these mechanisms might have operated simultaneously.
The regressive hypothesis suggests that some bacteria living as parasites continuously lost their complexity through evolution, even discarding their ability to produce proteins. Luckily, the host's protein-making machinery matched theirs, allowing them to ultimately become viruses. But these crippled parasites could only live within specific hosts, as only there were the corresponding types of protein workers to produce necessary materials.
Evidence for this hypothesis comes from chlamydia, an intermediate form between viruses and bacteria. Chlamydia cannot survive independently in the environment and must rely on a host for reproduction. It still retains a cell wall and can be killed by antibiotics, unlike true viruses.
The second hypothesis, the DNA escape hypothesis, posits that viruses could evolve through non-biological evolution, meaning a segment of escaped genetic material evolved into a virus.
As mentioned earlier, bacteria undergo horizontal gene transfer, a process akin to injection, with one bacterium extending a long, hollow tube into another and injecting a segment of its DNA.
Most eukaryotes don't transfer genes this way; they have a more advanced method
Even more, there are "retrotransposons," which don't operate on Ctrl+X and Ctrl+V but on Ctrl+C and Ctrl+V, copying a segment of genes and finding a place to insert it in the DNA. Over millions of years, some misinserted fragments floated away. If they retained the ability to produce a protein shell, viruses emerged.
The third hypothesis, spontaneous generation, includes the most evolutionary perspectives
In 1965, Sol Spiegelman, a biologist at the University of Illinois, discovered a strange phenomenon while studying RNA replication. He used a bacteriophage (Qβ phage) with a DNA sequence length of 4500, adding sufficient raw materials, i.e., free nucleotides and some RNA replic
ase, to a test tube and mixing them thoroughly. With ample materials and protein workers, one would expect a large quantity of 4500-length RNA, right?
Spiegelman aimed to replicate a massive amount of RNA sequences artificially. Periodically, he transferred some RNA from one test tube to a new one filled with raw materials. He found that the RNA sequences became shorter with each transfer, from 4500 to a few thousand, and then to a few hundred. By the 74th tube, there was only one kind of RNA, 218 nucleotides long. After many attempts, the outcome consistently stopped at 218 nucleotides. What does this 218-length RNA do? It continuously replicates itself using abundant nucleotides and replicase in the environment. Except for not creating its protein shell, isn't this essentially a virus?
Later, Manfred Eigen's laboratory in Germany improved this experiment. They didn't even add the bacteriophage's RNA, only its replicase and a bunch of nucleotide materials. After several generations of evolution, the improved experiment produced two RNA lengths — one 48 nucleotides long and the other 54 nucleotides long. What are these nucleotide lengths? One is for HIV-1 reverse transcriptase, and the other for another type of RNA polymerase (T7 RNA polymerase). In other words, given enough materials in the environment, virus sequences could emerge directly.
Whether in biology or non-biology, absorbing energy to create order is an unstoppable trend, from the crystallization of small molecules to the replication of viruses and microorganisms, and even to the structure of human society.
Alright, that's all for today. See you tomorrow.