At long last, we return to the exploration of multicellularity that was started a few weeks ago. In Part I, I discussed the fact that multicellularity, the ability of many cells to act as one, is something that can evolve when a single-celled organism experiences selective pressure, like predation. Part II was an exploration of multicellular behaviors, and how organisms that have been traditionally considered unicellular - bacteria and slime molds in particular - actually behave in ways that can be interpreted as multicellular. In Part III, we took a step back and consider the definition of “life” in the first place. 

Today we are going to focus on understanding the difference between eukaryotes and prokaryotes. The evolutionary differences between these two categories can easily be seen by looking at a version of the tree of life:

In this 30,000 ft view, prokaryotes are represented on the far left, as “bacteria and archaea.” They are the most ancient roots on the tree of life, the origin point form which all other life has sprung. These are cells that lack internal, specialized subunits, though they do have the pieces fundamental to all of life - DNA, RNA, protein synthesis, and ATP production. What they lack is the organizational intricacy possessed by eukaryotic cells, which occupy the rest of the tree. Looking at this phylogenetic representation fails to capture the scale of differences between prokaryotes and eukaryotes, save for the fact that prokaryotes are older and less numerous than the other branches. 

In order to take a closer look at those, it helps to take a look at David Goodsell’s work. He’s a professor at the Scripps Institute of Oceanography who has devoted himself to illustrating biological objects - from proteins to cells. In his book, The Machinery of Life, he breaks down the components of cells, how they fit together inside of a living organism, and offers a unique perspective on what is going on inside of cells. Below is an image of an Escherichia coli cell, a mainstay of laboratory research, taken from his book. 

From this illustration, it is apparent that E. coli is a relatively simple cell. It’s pill-shaped, with multiple flagella projecting off of the cell surface. Inside Goodsell has painted molecules of water, proteins, and a large wad of knotted genetic material at the center. There are exceptions to this kind of structural organization in the bacterial world, but setting aside periodic exceptions, this is standard fare. What about eukaryotic cells? 

Go looking for a comparable Goodsell illustration of a eukaryotic cell, and you won’t find one. This isn’t because he hasn’t made one, he has made many. It’s because, as he says in his 2011 paper, Eukaryotic Cell Panorama, “eukaryotic cells are typically too large to show in their entirety and still show individual molecules: at 1,000,000 X magnification, the entire cell would be several meters wide.” To represent something so massive, he has to break the cell down into component parts, highlighting processes and regions, rather than representing the entire object at once. Below are several panels of his Eukaryotic panorama, taken from The Machinery of Life. 

The enormous size of eukaryotes is apparent even in the oldest, single-celled varieties, called protists. These are strange and abundant creatures that have been found in freshwater ponds for as long as microscopy has been around. These little creatures represent the simplest form of eukaryotic complexity. Though they are a far cry from even the simplest plants in architectural complexity, they can shed some light on the fundamental principles that separate eukaryotes from their prokaryotic cousins. 

Take, for example, the process of eating. Though bacteria take up nutrients from their environments, they don’t “eat” in the same way that we do. Prokaryotes depend on nutrient sources that have been broken down into the most simple forms available. If a pre-digested food isn’t available in the environment, bacteria will release enzymes that break down larger particles into the kind of scales that can be taken up by the cells, molecule by molecule. On the other hand, eukaryotes are capable of eating creatures that are smaller than them - amoeba or bacteria - and digesting them in acidic compartments. Once the food has been broken down, the parts are distributed throughout the cell where they are most needed - for building proteins, replicating DNA, making repairs. It’s a process that’s far more intentional than the simple diffusion model that we think is happening inside of prokaryotic cells. 

Eventually, this sort of single-celled complexity transforms into a scaled version of itself. Organelles remain on the cellular level, but are mirrored by organs on the organismal level. Specialized body compartments appear that are reflections of cellular structures. Calcium-based bones mirror actin scaffolds, muscles represent enormous superstructures of contractile filaments. Nerves, isolated wires for transmitting electrical signals are similar to the filamentous projections of slime molds and mushroom mycelium. Eventually, there evolves a control center that moves up and away from physical processes, a governing circuit that gives birth to homeostasis and autonomous function. How does this come to pass? 

Understanding the answer to this question requires piecing together a puzzle that is missing many pieces. Presently, we can only directly observe a snapshot of outcomes. What I mean by this, is that we have a readout of what some 4.3 billion years of evolution has produced, but a very rudimentary understanding of how these forms came to be. We depend on the interpretation of a fossil record, ancient scars in rocks, sedimentary layers at the bottom of the ocean, etc. As far as I can tell, scientists have not found any intermediate forms - eukaryotes with more than one cell but fewer than a few hundred. 

Perhaps this is because they haven’t been looking hard enough, or in the right places. If this is the case, then it is a question that can only be answered through the resurgence of citizen science, like that advocated for by Mary Ellen Hannibal. If intermediate organisms are out there, they may be rare and occur only in a narrow window of specialized conditions that have, to this point, been overlooked. 

Another possibility is that complex eukaryotes emerged at a specific time in Earth’s history, in conditions that have since vanished from the surface of the earth. Evidence in support of this It may be that the intermediate organisms are out there, but they are rare and only occur in highly specialized conditions and so have been overlooked. Though we cannot accurately estimate what these ancient conditions may have been - though many are dedicatedly trying - scientists do have some sense of a seminal event in the evolution of complexity. 

One important step is the appearance of the compound cell - one that contained mitochondria, a specialized unit for producing fuel. Lynn Margulis, then Sagan, proposed a version of events in her paper On the Origin of Mitosing Cells. At 56 pages it is a dense read, but is a comprehensive answer to the question of how eukaryotic cells could have emerged from prokaryotic cells. Her answer? Endosymbiosis.

The theory goes that photosynthesis evolved early in the history of our planet - and a byproduct of photosynthesis was the emergence of large quantities of oxygen. Oxygen, in large quantities, is corrosive and toxic. This led to a selective pressure that forced organisms to adapt - either they relegated themselves to the corners of the earth that didn’t have any oxygen, or they found ways to deal with its corrosive effects. 

The previous discussion of the Deep Biosphere suggests that many organisms devoted themselves to niches far away from oxygen, but a second solution came out of an accidental combination, where “an aerobic prokaryotic microbe (i.e. the protomitochondrion) was ingested into the cytoplasm of a heterotrophic anaerobe. This endosymbiosis became obligate and resulted in the evolution of the first aerobic amitotic amoeboid organisms.”

The mitochondrion would have been a bacterium capable of using oxygen to perform the reactions of life, thereby benefiting it’s host in two ways - sucking up the excess oxygen, and spitting out ATP, the ubiquitous currency used for performing cellular functions. Margulis, though, didn’t stop at the level of the mitochondrion. She suggested that “The diversity of cell structure and the life cycle in lower eukaryotic algae imply that different photosynthetic prokaryotes (protoplastids) were ingested by heterotrophic protozoans at various times during the evolution of eumitosis.” 

Though her theory of how motility and chromosomal division came from an amoeba absorbing a flagellated bacterium occupy the bulk of her original paper, it is the mitochondrial theory that has stolen the spotlight. In some ways it makes sense - the flagellum doesn’t seem to have it’s own genome, making the story of how it came to be more complex, and less straightforward on an evidentiary level.

The last piece of the puzzle is understanding how a complex organism, like a fish, sea sponge, coral, or human could have possibly emerged from a single-celled eukaryote. To my knowledge, Margulis doesn’t explain this, but it seems like what we know about single-celled bacterial behavior can inform our visualization of the emergence of true multicellular complexity.

Even in bacterial biofilms, dense assemblages of prokaryotic cells, we have evidence of hallmarks of true multicellular behavior. There is the production of specialized architectures in the form of structural matrix proteins, cellular differentiation mediated by environmental conditions, and even cell death. Sexual reproduction is absent in the true sense - but free exchange of DNA on plasmids and mobile DNA elements means that clonal populations persist for some time before being replaced by a slightly different genetic background.

If a bacterial cell and archeal cell came together to produce a eukaryotic cell, this new cell would likely maintain generic multicellular behavior for some time. In that context, the dense conditions of a proto-eukaryote biofilm would lead to the production of a very basic multicellular organism. If that organism acquired the ability to reproduce itself from a single cell, reliably, every time - then suddenly a single cell has become an organism that serves as an evolutionary unit, subject to the same selection pressures experienced by other organisms.

Over time, this new organism went from being multicellular-like to being truly multicellular and, in some ways, immortal. Even in eukaryotes the combination of gametes - sperm and egg - produces a new organism that starts from zero, with the slate of time wiped clean. This regenerative ability is an important reason why multicellular eukaryotes have managed to branch out into so many different forms, as represented by the tree of life at the beginning of this article. The organizational unit - the multicellular organism that can produce vast amounts of useable fuel because of a synchronous symbiotic event - is the metabolic backbone that has provided for this explosion of variety.

Parting Thoughts

One question that still concerns me is whether or not this process is still happening beneath our noses, or if it was a one-off- a happy accident that depended on the combination of two perfect cells that were able to work together like none before them. The timespans involved in this formation, the hundreds of millions of years - maybe even billions of years - make the assessment of “is this happening right now” really difficult.

Timescales of that size have a way of erasing incremental change, so we have a hard time looking at the current state of biology and evaluating if this is actively happening. But given what we know about novel endosymbiotic events - such as the intestinal bacteria of mealybugs, where a novel symbiosis event appears to be happening beneath our very eyes - it seems like it could be happening around us, nearly undetected.

Overall, the question of multicellular complexity and the emergence of eukaryotes is a fascinating one, filled with big questions about complexity, form, and function. The metabolic flux provided by the appearance of mitochondria allowed cells to grow larger, and their bacterial roots allowed them to form more complex structures. Eventually, these new organisms must have evolved the ability to reproduce themselves from a single cell. It isn’t much of a stretch, since a bacterial colony can already do that! 

Sexual reproduction, the fusion of cells from two different colonies to produce one that didn’t look exactly like either precursor, would have been the very last step. Once that was in place, this new lifeform would have been able to evolve as a single unit, and would have been able to differentiate into the variety we see today - including the single-celled eukaryote that manages to do everything itself. 

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