Could Enzymes Be Considered Organisms? Exploring a Bold New Theory
Here’s my argument for why I think they just might be
I asked my lecturer if viruses were alive.
His response didn’t surprise me. I have heard and read about it a dozen or so times. The principal argument is that viruses lack the replicative material found inside cells. They have the replicative potential but absent the machinery, they are functionless.
Forterre, however, has a different opinion on what viruses could actually be. His argument is sound. It considers cells without the virion particles as ribosome-encoding organisms (REOs). Those that are infected by viruses are capsid-encoding organisms (CEOs). He then flipped the concept and called CEOs viruses. The genetic products are just the particles they secrete in the same way other cells secrete proteins. He then goes on to give a logical argument for why this paradigm shift settles many of the scientific debates.
From such a flip of ideas enters my argument about enzymes, which could be organisms. An enzyme is very different from a virus (CEOs or capsid-coated genetic products) in the sense that it doesn’t have a genetic code.
How then could an enzyme be considered an organism?
I’ll take you back to an age-old mystery that I bypassed to make my argument.
Guess who’s back?
Guess who’s back? Guess who’s back?
Guess who’s back? Guess who’s back?
Guess who’s back? Guess who’s back?
Guess who’s back?
What’s back is the question — What is life?
I don’t know. Neither did Erwin Shroedinger. Anyone who claims to know what life is is either deceiving himself without knowing it or on a mission to deceive others. The first rule is never to deceive yourself, and you’re the easiest person to deceive.
Thus, I cannot make a logically airtight argument for why I live. Living beings appear to have crossed a certain threshold where we can thematically conclude that they are living. Making such an argument for enzymes is bonkers.
So I avoided it altogether.
My argument is not on whether enzymes are ‘living’ organisms, but why they are organisms. I define organisms as physical entities that struggle to avoid annihilation. This simple definition encompasses every physical material you can think of, from quarks to black holes. Even cities have the behavior of organisms.
A cell tends to avoid annihilation. It has systems and processes to do just that. A gene, the physical portion of DNA, tends to avoid annihilation through its processes of genetic inheritance. However, even with our DNA, our coherent and lucid selves would be impossible without enzymes.
DNA generation requires an enzyme. DNA correction mechanisms require enzymes. Enzymes are physical entities that tend to avoid annihilation by serving their enzymatic roles. The cell, thus, preserves them because the cell needs these entities to survive. For one to survive, the role of one subcellular component has to serve the other and vice versa. The result is a stable and meaningful merger.
In a housed environment such as a cell, the enzymes serve the genetic material. The genetic material serves the enzymes by generating some of them and also by shielding them from the harsh environment outside the cell.
The mishmash inside a cell has the right settings for enzymes to thrive. The pH and the temperature dictate how effective, or lack thereof, an enzyme is. The merger between the cell and the enzyme, and the enzyme and the genome helps create the systemic entity capable of Darwinian evolution.
Furthermore, if an enzyme is an entity that tries to avoid annihilation, then its role gives the clue away — enzymes are entities that expedite reactions without taking part in them. They are effect modifiers. However, their structure doesn’t change. Isn’t that an ability to avoid annihilation?
Based on this definition, enzymes can be considered organisms. Not living organisms — just organisms.
Now, among the enzymes that fascinate me is one involved in DNA replication that behaves most peculiarly.
Now this looks like a job for me
A visionary, vision is scary
Could start a revolution, pollutin’ the airwaves
A rebel
This vision can be scary because I’ll be making an argument for enzymes different from what the biological field agrees on. Anyway, I only have one life — might as well make my case. It could start a revolution, or it could sink into the deep abyss of articles churned every second all over the globe. Furthermore, I have not published this idea in peer-reviewed journals. Yet. Regardless, since this article is more accessible, more readable, and more open to a wider audience, it can serve as a proxy for what is yet to come.
Now, the enzyme that fascinates me is the DNA polymerase. Our current understanding of how this enzyme works is in the synthesis of nucleotide bases at the points where the DNA is unwound by yet another enzyme—the helicase. Furthermore, much of what we understand about the replication process is from our model organism, E. coli. Basically, bacteria have taught us more about DNA than other model organisms, and in particular, the DNA replication process.
The DNA polymerase has subtypes 1–5. The polymerase 3 is the subtype involved in the synthesis of nucleotides and their subsequent bonding as it moves like a zipper from one prime end to the other. Usually, it moves from the 5 prime to the 3 prime end. DNA replication cannot happen in any other direction. It’s the one-way valve of genetic replication.
But besides generating new genetic material, this enzyme has another function — eliminating errors. Recall that I’ve just told you that DNA replication only happens from 5 prime to 3 prime. However, the other function of polymerase 3 is it removes mismatches noted along the replication strand.
Let’s say, for instance, A which should be paired with T becomes paired with G. If this is detected by the enzyme polymerase 3, it does something remarkable. It basically says:
Now this looks like a job for me
It reverses its direction from 5 prime to 3 prime, does a complete 180 degrees, and moves from 3 prime to 5 prime just so it can remove this mismatch. This ability is the other function of polymerase 3 — exonuclease. Exo- to mean exclude and -nuclease to show the active role of the enzyme in removing this nucleotide base. Thus, the enzyme has two principal roles — synthesize a new DNA strand, and remove mismatches.
Think about it for a minute. First, there is only one way DNA strands can form. From 5 prime to 3 prime. But this enzyme does two peculiar actions — it ‘detects’ a mismatch.
Detects.
Let the word sink.
Detection is a cognitive function. We detect the presence of another organism by sensing its presence through our sense mechanisms. This enzyme detects that there is a mismatch.
The other phenomenal task it does is it pauses its initial role, goes back, then removes the mismatch and corrects it. This can only happen when there is an understanding of what it considers appropriate and what it doesn’t.
Note that this is a protein. It doesn’t have any genetic code inside it. It doesn’t have any cellular mechanisms inside it. Just folded protein. But it detects the mismatch in the same way you can detect something crawling under your skin. Isn’t that organismal behavior?
If this doesn’t blow your mind away, then my guess is you haven’t fully grasped the concept I had in mind. Probably. Furthermore, I have mentioned that organisms are physical entities that tend to avoid annihilation. If the DNA is poorly replicated, the enzyme’s safe house is at risk. To avoid doing that, it has to correct the mistakes it can correct. The role of the enzyme is to serve the cell. In reverse, the role of the cell preserves the enzyme. A stable merger is preserved and both entities live to see another day, in whichever time sequence one considers.
Effortlessly, the enzyme echoes the lines by Eminem:
But no matter how many fish in the sea
It’d be so empty without me
What I’m trying to say is…
Enzymes are organisms based on the Organismal Theory of Evolution. So…
Here’s my ten cents, my two cents is free
This piece highlights my ten and two cents on enzymes. But there is more about DNA replication and enzymes that I have glossed over, such as Eigen’s threshold, which is not the argument of this article. Regardless, I hope I have somewhat made you consider the possibility that an enzyme could be an organism.
Not a living organism.
But an organism with key organismal tendencies.
