Despite appearances, up until this point I have actually given evolution quite an easy time. I have shown that, under certain strict conditions, the information for small microproteins in bacteria could potentially evolve from scratch within a reasonable evolutionary timeframe, although how they acquire address labels is more problematic. But these are relatively simple problems compared with the next level of complexity found within cells.
There are two main types of cell – “prokaryotic” and “eukaryotic” – with a number of important differences between them. “Prokaryotes” are single-celled organisms, while eukaryotic cells are usually part of multi-cellular organisms, called “eukaryotes,” and their cells are much bigger than a prokaryotic cell.
Prokaryotes such as bacteria have a circular genome, with one or two “chromosomes” that contain the organism’s genetic information. Eukaryotes have genomes that are broken up into many linear chromosomes, allowing for a much larger information storage capacity. For example, this structure enables the human genome to contain over 3 billion pairs of nucleotides.
Eukaryotic cells also contain “mitochondria.” These convert oxygen into chemical energy, providing a power source for much of the cell’s activities, allowing them to do much more than prokaryotic cells.
Mitochondria contain their own DNA sequences, called “mitochondrial DNA” or mtDNA for short. Human mtDNA is made up of over 16,500 nucleotides in a circular, double-stranded DNA molecule, similar to those found in bacteria. This contains genes that make up what is called the “electron transport chain,” in which electrons are passed around to fuel proton pumps that create energy for the cell. The mtDNA also contains genes to make two major parts of a ribosome, and 22 genes for tRNA molecules that contain the genetic alphabet.
One evolutionary story of how mitochondria came to be goes like this: there was once a bacteria that invaded or was somehow engulfed by another prokaryotic cell, and gradually the invader merged with the host to become part of it, in a process biologists call “symbiogenesis” or “endosymbiosis.”
How does one organism engulf or invade another, and get passed on with the offspring? If you swallowed a mouse, or one somehow managed to find its way into your gut, any future children you had wouldn’t have little mice in their gut.
On the other hand, trillions of bacteria live with us, often doing useful things. For example, lots of them live in our gut, helping with digestion, in a form of what is called “symbiosis,” where two or more different organisms live closely together in a helpful relationship. The important thing here is, our gut bacteria remain their own organisms. They are passed down from mother to baby, and this is usually beneficial for the baby.1
However, mitochondria aren’t separate organisms. They are little organs (called “organelles”) in a cell. The blueprints for their manufacture are written into the genome of an organism. The key question here is, how did a bacterial invader go from being an independent organism living in a host cell, to an organelle coded for by nucleotide sequences in the offspring of the host?
According to the evolutionary story, at first the invading or engulfed bacterium divided independently of the host cell, making many copies of itself, which would perhaps explain how it was able to get into the host cell’s offspring. When the host divided, some of the invader’s offspring found themselves in the daughter cells.
Next came the serendipity wand of translocation. The offspring of the invader fired off bits of their genome, and these were gradually incorporated into the host cell’s genome, perhaps through the use of a DNA repair mechanism. A number of unspecified magical steps then occurred, assembling these bits over time into mitochondria by the host’s genome. Evolutionary theorists assume that most or all of the invader’s genome was translocated over to the host, but that most of it later mutated away, leaving only a tiny core of mitochondrial DNA that has been preserved by natural selection.
The evolutionary story skips over the exact step-by-step details of how this method of DNA acquisition can, over time, completely turn pieces of living bacteria into a cell battery. It would be like gradually salvaging parts from a shipwreck, only to find later that they have been assembled into a speedboat. The story also fails to tackle how all the parts acquire completely new address labels to assemble themselves at a specific place in the host cell, and how the host builds a blueprint to achieve this assembly.
Other research has challenged this story. Bacterial ribosomes are made up of about two-thirds RNA and one-third proteins, but this ratio is reversed in the ribosomes of mitochondria.2 Plus, the link that supposedly connected mitochondria to bacteria isn’t anywhere near as close as had been assumed.3
Furthermore, based on protein “superfamilies” – that is, groups of proteins that are assumed to be related – the code making up mitochondria couldn’t have come from an individual bacterium, because half of the superfamilies aren’t found in any one bacterium. However, they do occur in what is called the “universal common ancestor,” the hypothetical ancestor of all organisms. As a result, some researchers argue that the mitochondria simply evolved in the more traditional manner.4
If mitochondria aren’t engulfed or invading bacteria that turned into cell batteries after all, this shows how an evolutionary story can capture the minds of scientists, even if it turns out later to have been pure fiction.
But putting aside the exact way mitochondria are alleged to have evolved, and looking at them from a design perspective for a moment, why would they contain their own DNA molecules?
Since mitochondria are the powerhouses of the cell, their functions are critical. If they stop working, the cell dies. Their miniature DNA strand contains genes for their own version of a ribosome, which in turn produces many of the components needed to make power for the cell. This means mitochondria can repair and renew their own machinery quickly and efficiently. They don’t need to wait for the cell to send the components. Instead, they can manufacture them locally, saving critical time if anything goes wrong. This certainly makes for a good design feature.
Whatever the case, animal, plant and human life couldn’t really exist without mitochondria. They provide the energy needed to support multi-cellular life. And this isn’t the only “lucky” innovation for the eukaryotic cell.
In prokaryotic cells, the DNA molecule and the ribosomes are all in the main body of the cell. By contrast, eukaryotic cells – the cells of all plant, animal and human life – have an inner compartment called a “nucleus,” which contains the DNA molecule and keeps it separate from the rest of the cell.
The nucleus is surrounded by a double membrane called the “nuclear envelope,” which contains hundreds of channels called “nuclear pore complexes,” or “NPCs” for short. Like cherubs guarding the entrance to Eden, NPCs control the entry and exit of large molecules through the nuclear envelope. The average NPC is built out of about 1,000 proteins that biologists call “nucleoporins.” Many of these work together to form smaller units within the larger structure.
In an earlier chapter, I discussed how a sequence of DNA is transcribed, to create a strand of mRNA that provides the code to make a protein. I compared the DNA molecule to a library of books that couldn’t be removed from the building. If you wanted to read a particular book, you needed to make a photocopy.
In eukaryotic cells, the “photocopy” of a DNA sequence is made inside the nucleus, as a strand of mRNA. The mRNA must then pass through one of the nuclear pore complexes and into the main compartment of the cell, the cytoplasm, before it can be translated into a protein.
To pass through the NPC, an mRNA strand is given the equivalent of a ticket that allows it to enter the central channel. Once it reaches the other side, it must give up its ticket, preventing it from re-entering the nucleus.
The presence of mitochondria, a nucleus and NPCs are defining features of eukaryotic cells. They are present in all plant, animal and human life. Clearly then, they are critical for creatures made up of more than one cell. Their core functions are virtually identical across the spectrum of eukaryotic life, with only fairly minor variations in species that are supposedly separated by a billion or more years of evolution.
Theorists assume these things must have evolved in or prior to what they call the “last common ancestor” of all eukaryotic cells, a particular ancestral cell that somehow bridged the gap between prokaryotes and eukaryotes.
The invention of a nucleus and nuclear pore complexes somewhat shields the DNA molecule from outside influences; but ironically, evolution needs this influence to produce large-scale changes. In other words, these new cell features should have put a substantial brake on evolution. Instead, what we see is an explosion of life based on this cell design. Either way, let’s now turn our attention to building a nuclear pore complex.
1 See the article “Like Genes, Our Microbes Pass from Parent to Child” by Martin J. Blaser, published at scientificamerican.com on March 1, 2015. 2 Sharma, et al, “Structure of the Mammalian Mitochondrial Ribosome Reveals an Expanded Functional Role for Its Component Proteins”, Cell, 2003. See the “Introduction” section in particular. 3 See the article “Mitochondria’s Bacterial Origins Upended” by Shawna Williams, published at the-scientist.com on April 25, 2018. 4 Harish, Kurland, “Mitochondria are not captive bacteria”, Journal Of Theoretical Biology, 2017. See also the article “Overthrowing the Hegemony of the Culture of Margulis?” written by Susan Mazur, published at huffpost.com on August 22, 2017.