Basics of Evolution

This is an excerpt from the book series Philosophy for Heroes: Continuum.

What are the three major properties a system needs to have in order to evolve?

Still, it needs to be said that the light of evolution is just that—a means of seeing better. It is not a description of all things human, nor is it a clear prediction of what will happen next. —Melvin Konner, The Tangled Wing [Konner, 2003, p. xviii]

The purpose of the theory of evolution is to explain the wide array of life forms on Earth. Knowledge about the origin of species allows us to better understand why a particular organism has certain properties. While this is often obvious by looking at the environment of an organism, for example by looking at the teeth and the food, or the leaves and the precipitation and angle of sun rays, more complex behavior seems baffling, especially that of humans. Why and how did humans develop? Why do we have such a big brain? What is the reason for our behavior? All these subjects can be better understood when we understand our past—how life, and humans in particular, developed on Earth.

He who does not understand the uniqueness of individuals is unable to understand the working of natural selection. —Ernst Mayr, The Growth of Biological Thought [Mayr, 1985, p. 47]

Despite its very basic mechanics, evolution is a complex concept, requiring that we approach it in several steps. We will start where the first book left off: entities, properties, systems, aggregates, etc. This provides the philosophical foundation of the theory of evolution. In later sections of this chapter, we will take a look at chemical evolution, artificial life created by computer and ultimately the origin of life on Earth, evolution in our immune system, and evolution in our head.

Selection of Systems

Before we discuss evolution in detail, it is important to note that parts of the evolutionary process can be applied not just to living organisms, but also to any system—for example to chemical systems, simulated life forms in a computer simulation, or thought patterns in the brain. One of these parts is the selection process. To understand selection, let us revisit some of the definitions from the first book and add some new ones:

AGGREGATE ·  An aggregate is a number of entities that have a reciprocal effect on one another, so that they can be considered collectively as their own entity (e.g., a cup full of water—all water molecules interact with each other).

STRUCTURE ·  A structure is a description of required properties, dependencies, and arrangement of a number of entities (e.g., cube-shaped).

SYSTEM ·  A system is an aggregate with a definite structure (e.g., an ice cube is a system of frozen water molecules).

PROCESS ·  A process describes the mechanism of a cause working to an effect (e.g., if you put an ice cube into a glass of water, the cooling of the water is the process).

TIME ·  Time is a measurement tool to put the speed of processes in relation to each other.

PROCREATION ·  Procreation is a process by which a system creates (on its own or with the help of the environment) a new entity with a similar or (preferably) the same structure as itself.

GENERATION ·  A generation is a set of systems during one cycle of procreation.

GENOTYPE ·  The genotype is a system that is the blueprint for the phenotype.

PHENOTYPE ·  The phenotype is the actual body of a life form. Changes in the phenotype generally do not have effects on the genotype. Generally only the phenotype interacts directly with the environment.

MUTATION ·  A mutation is a change of the genotype of a life form. This change can, but does not necessarily, have consequences for the phenotype.

Mutations

Mutations, as our common knowledge suggests, are generally bad. No matter their effect for the overall population, for the individual life form, mutations are unwanted accidents. They happen, but they are not intended. An individual life form which is adapted to its environment does not want change. If the parent generation already has well adapted genes, the last thing they want is their offspring to have random changes. The only situation where (more) mutations are welcomed is when the life form is in a tight evolutionary race like a virus with its host—we will talk in Section 4.5, “The Red Queen Hypothesis,” about this situation and how life copes with it. But usually, the environment changes slowly enough that mutation is not a limiting factor.

Sometimes, multiple repair and protection mechanisms are bypassed by a mutation while it also is mutated in a way that it does not stop reproducing: that is cancer. To understand cancer, you have to understand multicellular organisms. For a single-celled life form, there is no such thing as cancer. Cancer is simply an unlimited self-replication of a cell. While this is exactly what you want for a single-celled life form, it possibly destroys the structure within a multicellular organism. If all of our cells divided uncontrollably, we would not survive. Our life depends on a highly organized and controlled process of cellular growth and death. Cancer for us occurs when those processes fail for a single cell.

Example When making a copy of themselves, most of our cells lose a few genetic base pairs at their ends. Once they have lost a certain amount of code, they stop duplicating themselves. Any damage of a defective cell would then be limited by its remaining duplication cycles. Any form of cancer cells would need to have undergone a mutation that fixes the ends of its genetic code after each duplication [Shay and Wright, 2011]. In a similar fashion, there are other protection mechanisms in the cell that a cancer cell has to overcome. For example, scientists have found that there is a single gene regulating multi-cellularity in organisms. It acts like a brake to stop multiplication at the right times. If that gene is defective in a cell, it might end up multiplying indefinitely and cause cancer [Hanschen et al., 2016].

Selection

FITNESS LANDSCAPE ·  The fitness landscape is the sum of all environmental influences on an entity. For example, if you are sifting sand, a riddle screen lets small particles of sand fall through while larger stones are retained. In this case, the riddle screen and the shaking of the riddle screen would be the “fitness landscape.” In nature, the fitness landscape would simply be the environment over time, including all other life forms, the climate, etc.

SELECTION (EVOLUTION) ·  Selection is a process where some (or all) of a set of systems of similar structure are retained while the rest are discarded or destroyed. Which ones are retained and which ones are discarded depends on the relationship between the structure of the individual systems and the fitness landscape. In the example of the riddle screen, the screen lets small sand fall through while it “selects” larger stones.

Selection is a central element of evolution. It connects systems with environmental factors. When the environment changes, different systems are selected. In order for selection to work—or to make any difference or sense—there needs to be variation. As such, the mutation rate of a population is caught between two conflicting forces: the tendency to replicate what works and fix any copying errors, and the need for some variety in the population in order for a population to evolve.

Nature’s solution for the conflict between variety and preventing errors was to keep mutations as low as possible, while using sexual recombination at the same time. Like mutations, sexual recombination keeps up the variety within a population. But it also kept individual genes intact, reducing the probability for destructive changes: it simply recombined working copies, resulting in a varied, but very likely functioning organism. It is hard to compare it to any everyday concept because it is a very unique solution. The closest analogy might be editing a movie where you cut and rearrange parts instead of trying to change individual pixels.

A population needs to have variations in order to evolve.

Example Imagine trying to sift identical stones with a fine riddle screen: nothing goes through. Or imagine trying to sift sand with a riddle screen: everything goes through. Likewise in nature, without change in the population, a population cannot move in any direction. If you use a finer riddle screen, more sand is retained. This changes the ratios between the different types of systems in the environment (for example the ratio between large stones and fine sand). Such changes could be caused by either selecting more (and discarding fewer), selecting fewer (and discarding more), or by selecting other (and discarding other) systems.

Example Imagine stones in a stream. The stones with the highest flow resistance experience the highest degree of erosion. They are “discarded” while rounder stones with lower flow resistance remain the same. Obviously, the “discarded” stones are not actually discarded but transformed into stones with lower flow resistance simply because erosion slowly removes the edges of those stones until they, too, become round.

The significant point is that selection applies to all things in the universe. It is simply a process describing the change of systems over time due to external influences by other entities. A system with lower “durability” will by definition not endure as long as a system with higher “durability,” so after a while, you will see the ratio of systems with higher durability increase. For this principle, we do not even have to look much at nature, as it is very much a logical process based on the properties of the involved entities.

But for evolution to happen, another component is necessary. The system needs to be able to “clone” itself and replace the systems that were discarded during the selection process. Looking again at our example with the stones in the stream, you can imagine that over time, the stones get smaller and smaller until only sand remains that gets easily pushed down the stream. With no new stones being added to the stream, all stones eventually will have turned into sand and washed away—even the ones that were least resistant to the flow. To clarify, sand and stones in a riddle screen do not “procreate” in any form, so while they undergo a process of selection, they do not undergo a process of evolution. You could argue that the stones in a stream adapt to their environment by replacing themselves with a rounder version, but this is a borderline case as erosion is very much a one-way street.

In order for evolution to occur, the life form has to be able to increase the number of copies of itself in its environment.

Selfish Genes

As stated previously, for evolution to work, selection needs to be—as the term suggests—selective. This means that selection needs to be based on an individual life form’s properties and not on a whole population of life forms. It is not enough that a change improves the ability for a life form to survive. It needs to improve the life form’s likelihood of survival relative to other life forms.

For example, if a life form has a mutation that produces chemicals that speed up the process of procreation but distributes these chemicals among all other life forms, every life form nearby profits, no matter whether they had the beneficial mutation or not. This is similar to the situation in an economy. Money, status, or reputation is given preferably to those people and companies that have methods more adapted to the environment (the market). A well-run restaurant with better service will attract more customers than a poorly run restaurant. If, at the end of the day, the better restaurant had to share its earnings with all other restaurants, it might have a harder time “evolving” and expanding its business.

Example An exception to the rule of having to work for one’s advantage are beehives. They consist of infertile worker bees and a single fertile queen. In this case, in terms of evolution, they can be seen as one large organism where individual worker bees have no problem sacrificing themselves for the greater good of the hive—if its queen survives, the worker bee’s genetic material survives. This idea is best explained in Richard Dawkins’ The Selfish Gene where he stresses how organisms tend to act primarily in favor of the survival of their genes, not necessarily of their own bodies.

With that, we arrive at a basic definition of evolution:

EVOLUTION ·  Evolution is the combination of the process of selection together with a system of cloning or procreation.

In order for evolution to occur, the life form has to be able to increase the number of copies of itself in its environment. In addition, the resulting population of life forms needs to have variation, and each life form has to be able to operate for its own advantage.

Randomness

There are many slopes leading up a mountain, but there are but a few mountain tops.

If it is all about variety, why do we still intuitively think that mutations are the driver of change and evolution?

It is easy to mistake mutations for somehow being the drivers of evolution. I cannot blame people who might do that. Sure, this misrepresents the theory of evolution, but it is ultimately the job of the proponents of the theory of evolution to make the right points. Similarly, it is easy to make the mistake of explaining evolution as if one type of organism mutated into another. But that explanation is like the many worlds interpretation, where our universe’s past has but a single deterministic history, but at each step, it looks like it could branch off into an infinite number of possibilities. Likewise, when looking back at your own ancestry, you see a long, unbroken string of ancestors who all successfully survived and procreated.

So, how do we approach this issue? Yes, mutation is part of the evolutionary process. And if we look back, we see ourselves as the product of a string of mutations. The problem with this approach is that it is a very anthropocentric view. What we need is a different perspective; we need to look at it not from the position of the “survivor,” but that of an outside observer.

From the outside, we see a population of individual organisms, with mutations causing diversity within the population. Over generations, the gene pool of the population slowly moves in a direction in which the organisms are better adapted to their environment. From this perspective, the driving force clearly is the environment. For example, let us say that within a population, there is one individual with a resistance to a certain disease. Over generations, his descendants will be more successful than other members of the population, so the gene with the resistance slowly spreads within the population until the majority has it. From there, another mutation might occur and spread in the same manner. Looking back, it seems that a single line of ancestors did all the “work” to find the advantageous mutation.

Evolution can be very predictable. For example, in nature, the problem of how to design a body or wings with low air resistance is solved again and again similarly because the underlying physics are always the same. There might even be only one (or very few) possible optimal solutions or paths to a problem so that you can even see identical genes in non-related species.

Example Imagine you have a mailing list with 10,000 addresses. You create two groups, sending half of them a message that you have a special ability to predict next week’s stock market and that a certain share will go up. Likewise, you send the other half a similar message, but tell them the share will go down. After a week, the stock will go up or down and either way, you discard half your list. To the remaining 5,000—the people whom you told correctly whether the share would go up or down—you will send another message, reminding them about your correct prediction. And you divide them again in two groups, telling one that a certain share will go up, and the other that it will go down. After a few iterations, the remaining group of maybe 100 to 500 people will think you are some kind of genius always making the right prediction. Similarly, when looking only at the results in nature, we might think that some kind of a genius has designed life on Earth. But it only looks this way because we ignore the number of times nature has produced results that did not survive to procreate.

Another factor in the preference for believing in mutations as opposed to adaption to the environment is that it leaves the door open for random events. But even if it is agreed that the environment is the driving factor of evolution, someone could argue that changes in the environment are random. But as we have discussed in the first book, Philosophy for Heroes: Knowledge: if (supposedly) “random” events were frequent enough, we always have found a pattern in the form of a natural law. In terms of evolution, one could argue that, yes, “random” events drive evolution through mutation, but these events are not frequent enough (yet) to be discovered by science and made into a natural law. Likewise, a changing climate because of a volcanic eruption is a “random event”—but only “random” insofar as we do not have the necessary data and do not yet understand the processes that led to such an eruption.

It appears that mutations are the drivers of change and evolution, because we are looking at our evolutionary history as survivors. Only if we ignore all the attempts of nature that did not lead to a successful organism, life looks as if it is driven by nothing but a series of miracles.

Evolution as Waves

Imagine sending 100 rats into a maze and then wondering if the one that finds the way out is some kind of maze-genius. But now (after all rats have left the maze) fill it up with water, and then cause some waves at the entrance of the maze until the waves have traversed through the whole maze to the exit. Would you think that those water waves are some kind of intelligent water molecules that found the right way through the maze? Obviously not, water waves simply expand into all directions and create the illusion that they are somehow intelligent. Likewise, populations in nature should be looked at as waves, with different members of the population being at different positions of the wave. Through their genetic diversity, they also expand like a wave, checking every direction for the “exit”—a genetic code that is better adapted to their environment.

This can be seen for example in a study made with E. Coli bacteria(see https://hms.harvard.edu/news/bugs-screen). The bacteria were spread on the left and right side of a large, rectangle shape petri dish. The petri dish was divided into different sections with no antibiotics, some antibiotics, and toward the middle 10x, 100x, and 1000x the amount of antibiotics. Over the course of 11 days, the bacteria evolved to gain more and more resistance until they hit the center. Mutated bacteria with significantly higher antibiotic resistance are able to enter a new sector. They are then the origin of a new wave of copies that are able to spread throughout the sector until hitting the next higher antibiotics barrier.

So, again, mutations (or recombinations and any process which affects the genotype or the process of phenotypical development) only create a variety of solutions, which then are selected by the environment. If mutations were the driving factor and not just the provider of variety, evolutionary development would work without selection by the environment: life forms would develop independent of their surrounding nature. If from this random evolution life forms developed that were as adapted as we see in nature, this, in fact, would be like magic and the idea of a supernatural, driving force behind evolution would sound more rational.

The only time when mutations actually drive evolution is when the environment changes in a way that a certain trait is no longer needed by the life form. If it no longer matters if a life form does or does not have a certain gene, any mutated version of the gene has the same probability to be selected or not. Over time, more and more mutations accumulate until the original gene has become more and more rare and ultimately disappears. An example of a purely mutation-driven evolution is an atavism. For example, sometimes, children are born with tails because the combination of the parents’ genetic remnants of a tail lead to a half-working copy of the genetic information of this limb of our distant ancestors.

“Macro-evolution”

Are larger mutations (“macro-evolution”) that suddenly give an organism a significant advantage an argument against the idea that variety is the driver of evolution?

While there is certainly enough literature on that idea in the fiction department, there is little evidence for the idea of “macro-evolution” in the real world but a whole number of arguments against it. First, there is no need for macro-mutations: all our organs can be explained by small evolutionary steps instead of large leaps. Second, any larger change to the organism affects all the parts of the organism which then have to be optimized again.

Imagine replacing the engines of an airplane with new, much larger ones. Sure, they are “better,” but now the wings have to be changed and the whole model of the airplane has to be redesigned, too. Not to mention the changed fuel consumption, or the change of the maintenance procedures. That “better” plane would probably not take off from the ground. Sure, after some iterations of optimization it might, but nature does not have the luxury to wait for a few generations until an organism is “tested” in the environment. Every single iteration has to be good, as evolution cannot back-track.

Turning the question about macro-mutations around, how did we acquire abilities that were only possible with multiple changes to the whole organism? For example, for spoken language, we need a specialized brain, a specialized throat and mouth, the ability to control our breathing, and language itself. If just one thing were missing, any of these changes would be worthless. Or would they?

One argument against evolution is that for such (and many other) functions, we needed large jumps to accomplish them. Basically, they look as if a designer knew what he or she was doing and created individual parts that fit perfectly together. With this “designer,” organs could evolve in anticipation of a newly desired trait in a later generation.

To argue against this point, it is necessary to understand how new traits can be added to an organism. The process of evolution at no point has the capability to “prepare” anything for some later generation, it needs to work now. In reality, it works the opposite way: evolution moves toward the point normally until all the conditions are right, and then a number of mutations combine the different existing abilities into a new one. Each step on the way contributes to a better organism, and each new generation afterward optimizes the newly found ability.

The point is that traits can develop even when there is neither a supernatural driver “directing” evolution, nor a specific requirement by the environment that puts a population under evolutionary pressure (like a predator). For example, spoken language certainly helped our ancestors, but it only started to actually develop once all the requirements were available. In biology, this is also called exaptation.

EXAPTATION ·  Exaptation is the use of a certain trait for a problem or environment other than what it was originally “intended” for. An example would be feathers that started out as heat insulation, and only later were used to improve jumping, and finally for flight.

In technology, this can also be seen with 3D graphic cards: 20 years ago, when the first 3D accelerator cards came to market, nobody thought about using them for complex problems of astrophysics, biochemistry [of California, 2012], cryptography, or the “mining” of virtual currencies. These functions piggybacked on the success of 3D gaming until the cards were so advanced that they could be used for other applications.

When examining the details, life looks anything but “designed.” There are too many strange design decisions, for example that the nerves of our eyes sit above our retina instead below it. This leads to us having a blind spot where the nerves lead back toward our brain. A designer would have done it the other way around, like it is in octopus’ eyes.

Likewise, nobody started out designing a 3D graphics card with the purpose of mining virtual currencies. Twenty years ago, that idea alone seemed ludicrous on multiple levels. But looking only at the present, the different technologies fit very well together, as if someone had planned out the whole thing from the beginning. In reality, the “planning,” for example in product development, usually leads to a product that looks very much “unplanned” and clunky. Hence, there is currently a transition going on away from classical planning from start to finish, and toward a more “agile” management method with many iterations. The reason this can be better is that during the development process, a company learns a lot of new things about a product, and the market and general environment change, too.

Looking at it from a different perspective, if we gave a truly good designer the task of creating plants that would still exist in 500 million years, the designer would rely on the theory of evolution. The designer would have no way to predict how the world would change over the course of 500 million years, so any form of “planning” would be fruitless. Instead of actually designing the biology of the plant, the only chance is to give it the ability to adapt to its environment.

Mutations that led to larger evolutionary jumps were always the result of many smaller changes. For example, the most recent mutation that enabled human language was prepared for by many other genetic changes (conscious breathing, descended larynx, etc.) with their own individual advantages.

In that regard, it is important to note that life on Earth is far from stable. We know of several extinction events in the last 500 million years that caused massive reductions (50 – 95%) in biodiversity within a relatively short time. Each event allowed species previously living in small ecological niches to become the most dominant species. For example, as a result of the Triassic-Jurassic event 200 million years ago that was probably caused by massive volcanic eruptions, all archosaurs but crocodiles and the bird-like avemetatarsalia from which stem all of the dinosaurs we know of became extinct.

Likewise, 65 million years ago, a massive asteroid impact near today’s Mexico caused the Cretaceous-Tertiary event which caused the extinction of the dinosaurs and gave rise to mammals. Other possible causes of massive extinction events are climate change, gamma radiation bursts of nearby supernovae, or life forms like the bacteria who first produced then-toxic oxygen, or terraforming humans today.

While we see massive changes of the ecology on Earth during these events, our previous discussion still holds. The changes are shifts not mutations within the populations. Suddenly, a single rare gene might have been the crucial factor that determined survival, so whatever other genes that individual organism had would spread as well.

It is not so much that evolution made a “jump.” It is simply that the environment and the factors influencing the evolutionary selection suddenly changed. This led to species on the fringes of the ecology suddenly becoming the most adapted species within their environment. These massive extinction events underscore that even under such circumstances, evolution still moves in relatively small steps.