Some people have anywhere from a slight misunderstanding to a complete lack of knowledge on how evolution by natural selection operates. I’m going to do a series on the subject to educate anyone who is confused by or interested in the theory of evolution.

Part 2: Evidence for Evolution by Natural Selection

Part 3: Higher Concepts in Evolutionary Theory

I am writing about the mechanisms of evolution first, and will later make a post on the evidence for evolution. I believe this to be the logical course to take, as the evidence will be more clear as to why it is evidence if one has a better understanding of how evolution by natural selection works.

The science of evolution by natural selection does not disprove the existence of God. Whether someone believes in God or not is a personal choice and it falls within the realm of philosophy, not science. Evolution is not concerned with how life came to be; that is a separate field called Abiogenesis. The phrase “On the Origin of Species” simply means that origin of species, i.e., the diversity of life. The science of evolution does not support an agenda of “social Darwinism”, and it is not concerned with the various philosophies based on it’s science.

Some Things To Know

Much of the current study of evolution is work done in genetics and biochemistry. In order for this to make sense, it’s essential that one knows the difference between what a gene is and what an allele is. Genes are the segments of DNA that a species shares – all humans share the same genes across 23 pairs of chromosomes. The differences between us are in the alleles. A gene is what codes for “eye color” while the different alleles of that gene are what code for “blue eyes” or “green eyes” etc. So, when it’s said that humans and chimps share 98% of the same genes, it’s because both humans and chimps have the same genes coding for protiens, with only 2% difference in the actual things that our bodies need to code for.

Although evolution often takes a genes-eye-view, most DNA is what is considered non-coding. Much of this non-coding DNA is involved in gene regulation. This includes promoters, enhancers, and introns. It’s actually very common for mutations and single nucleotide polymorphisms (SNP’s) to be present in these non-coding parts of the DNA as opposed to being in the protein-coding part of the gene (the exon). Furthermore, it is not always so simple as “allele A of gene R causes trait X.” Most traits are polygenic, and many genes are pleiotropic.

Evolution, in broad terms, is defined as the changes and differentiation in genes in a population that results in functional and/or morphological changes from generation to generation. Natural selection is defined as a natural process that results in the survival and reproductive success of individuals most fit for their particular environment.

New genes come about in a few ways. One is through random mutation of the DNA sequence in a gene, which alters the functionality of the protein it codes for. This functionality might be a change in what other proteins or molecules it can bind or associate with; gains, losses, or changes in mechanisms of enzymatic action; changes in stability; changes in solubility; etc. Another is through gene duplication, which can allow one copy of the gene to remain and continue its function while the other copy alters and takes on new functionality. This is something I saw in my own research, which the recently duplicated MED12 and MED13 genes into MED12L and MED13L, which are already taking on new functions.

Selection pressures are the causes in an environment that influence the allele distribution. In natural selection, selection pressures are those things that organisms must survive in order to reproduce and pass on their genes. This includes predators, availability of food, disease and parasite, changes in climate and geography, alterations to the environment (ie a new species moves in, a lake dries up, a species goes extinct etc).

How Evolution Works

The three observations that Charles Darwin observed that eventually led to the theory of evolution by natural selection are as follows:

1. Individual organisms within a species vary from one another.
2. Traits and characteristics are passed down to offspring through reproduction.
3. Organisms have more offspring than their environment can handle.

To break this down further, we first must consider the first obserevation. This seems painfully obvious – I am not an exact replica of my parents, and my siblings are not clones of me. We now know that this is due to independent assortment, random alignment, crossing over, as well as genetic mutation, which unfortunately Darwin didn’t have the advantage of studying. So already there is change occurring, and some of these differences will confer differential traits that are salient in survival and reproductive success in a particular environment.

The second observation tells us that there is some relationship between the parents and offspring – aka heredity. Once again, this is very obvious, but the true magnitude of this is easy to miss: we are not independent constructs, but must have had to inherit some fundamental part of ourselves from our parents, so that who we are (physically and mentally) is dependent on our parents. And, as a corollary, this tells us that the inherited traits which are salient in survival and reproductive success are passed down from parent to offspring, i.e., the offspring (has a good chance to) inherits traits from their parents that, in a particular environment, aid in survival and reproductive success.

The third observation is more difficult to understand, at least as far as how it is related to evolution. This is what Darwin observed that allowed him to come up with natural selection. Organisms have more offspring than the environment can handle because it is inevitable that some (if not most) will die. The offspring that did not die are the ones that had the traits (from observation 1) passed down from their parents (observation 2) that allowed them to survive better. The video below shows an example of organisms (mice) having more offspring than their environment can handle.

What is happening is that an organism gives birth to offspring that each have variations. Some of these variations will be more advantageous for survival, which will allow these individuals to survive longer and reproduce more. The often cited example is peppered moth in which a species of moth, which had variations between light and dark colored (with the vast majority being light colored, giving them camouflage on the light colored lichens on the trees). When factories moved into their habitat, the lichens died out due to pollution, so that the moths had to live on the dark colored bark of the trees. Because of this, the light colored moths were more easily picked off by predators, with the dark colored moths now having better camouflage. Over time, the dark colored alleles became the predominant features in the moth species, essentially changing the moths from light colored to dark colored.

Variations in individual organisms create changes, natural selection causes the changes that are best suited for a particular environment/ecosystem to survive and propagate those changes to their own offspring. Mutations and variations are like a tree branching out in all different directions, and natural selection is shearing off the branches less suitable for survival and allowing the more fit branches to continue growing.

Where each branch stops with a red X are where the lineages that were “sheared off” by natural selection. What is doing the “selecting” in evolution by natural selection? These are known as selection pressures. The most obvious and often used example is that of predation, wherein predators go after the “weakest” prey animals. The scare quotes around “weakest” is because, as we’ll see below, this is somewhat of a misnomer. The reason a predator might kill a prey animal could be for myriad reasons that do not have to do with the prey animals being “weak” in some way that humans use the term; the prey animal only need be less suited to the environment than other prey animals (of the same and/or other species). Likewise, this can apply to things like plants and fungi, for which human notions of “weak” and “strong” don’t readily apply. Thus, in evolution, the concept of fitness is used rather than “weakness” or “strength.”

Other common selection pressures are (including, but not limited to):

• Competition for resources from other organisms (of the same or different species) in the same niche
• Environmental/Climatological hazards (e.g., living on a mountainside vs. living in a desert vs. living in a rain forest; the frequency of storms or forest fires)
• Environmental/Climatological changes (e.g., an environment becoming drier or warmer; a river drying up; a new species moving in or a species leaving or going extinct)
• Diseases, parasites, and toxins
• Available food (e.g., the famous beaks on Darwin’s finches)
• Sexual selection (more on this in part 3 of this series)

The split-offs (in the above figure) happen when a population of organisms becomes reproductively isolated, which means that the population essentially splits into two. This causes the two populations of the same species to face different selection pressures. When the two groups are forced to overcome different selection pressures, the alleles and mutations that are best suited for survival will be different between the two formerly homogeneous populations. This causes different traits, behaviors, and characteristics to become more predominate in both populations. After several generations of different alleles and mutations being propagated through the isolated population, they eventually become a distinct species.

This is known as speciation.

Reproductively isolated does not necessarily mean geographically isolated (although this is the way it often happens and is the most obvious example of it happening). Organisms can evolve within the same geography if it is sufficiently large, or if two variations begin to fill a certain niche within the same environment (although the latter is rare).

But in order to truly understand how the great diversity of life arose on earth, one must have a grasp of geological time. The time scales involved are so vast that it can really only be grasped by analogy. If one were to stretch their arms out with the fingers extended and used the span of their arms to represent the time the earth has been around, the amount of time that modern humans have been on earth could be shaved off the fingernail in one swipe of a file. If one were to compress all time down into a single twenty four hour day, humans would not have even been around for the last minute.

We can therefore think of evolution by natural selection as a kind of iterative algorithm, where each iteration introduces some level of noise or randomness to the output of the previous iteration, and then the environment culls outputs that do not reach a certain threshold. Doing this over millions of iterations will lead to outputs at Z_1,000,000 that are very different from the first output at Z₁.

This was a very basic overview of how evolution by natural selection operates. It is, essentially, a very simple process, but even still it is not intuitively obvious (particularly when thinking about the time scales involved) and there are a lot of misconceptions about it. I will now go over some of the most common misconceptions.

Common Myths About Evolution

Myth 1: Evolution means only the strong survive
In this case, “strong” means those things valued by humans, such as being smarter, faster, stronger etc. A common misconception (propagated by this popular mantra) is that evolution is the process of making organisms “better”. The idea of better is difficult to define in a general sense. Better is true in the sense of being better suited to a particular environment or ecosystem or better yet a particular niche in a particular environment. But the popular usage generally suggests the stacking of traits onto an organism, much like an RPG game, where each species is attempting to get to “the highest level”. This is untrue in biological evolution, where traits that are better suited, regardless of whether they are more complex or “better” by the qualitative assessment by humans, are the traits that will become predominate in a species. This leads to point 2.

Myth 2: De-evolution
Evolution is not directional. There is no increasing or decreasing of evolution. If losing a trait allows an organism to survive better, it has evolved in that it has changed to better fit its environment. Evolution can explain why organisms can increase in complexity, but it is not necessarily an increase in complexity. Evolution has no goal. It is not trying to go somewhere. It is not attempting to increase complexity. Therefore it cannot “backtrack” because there is no backwards in evolution. There is no such thing as de-evolving.

Myth 3: If evolution is true, why are there still “lesser” animals?
This goes back to point number two, but it still requires further explanation. Like I said, evolution is not trying to achieve any sort of goal, it is completely passive. It has no foresight and does not anticipate any future changes. The form an animal takes is the product of the selection pressures its ancestors faced. A common question I’ve heard is “if humans and chimps came from the same common ancestor, how come chimps aren’t as smart as humans?” The simple answer is: chimps did not have to face the same selection pressures that humans did to become what we are today; chimps and their evolutionary ancestors faced different selection pressures. Chimps are suited for their environment; not all species are stumbling around in the dark on the path to becoming human.

Myth 4: Individual organisms can evolve
Evolution occurs on the scale of populations, not individuals. Once an individual organism is conceived, it has it’s specific alleles for the rest of it’s life (even epigenetic changes (see this video on epigenetics) occur within the realm of the organisms genes). Where the change occurs is during reproduction – the offspring has a mixture of it’s parents alleles and has accumulated genetic mutations (the rate of genetic mutation is relatively constant) – and in which individuals possess traits that have allowed them to live long enough to successfully reproduce.

Myth 5: Micro-evolution is happening, but not Macro-evolution
This is a common and relatively understandable misconception about evolution, since “macro-evolution” is not something that can really be seen in our everyday life. The simple answer is that “macro-evolution” happens on timescales that we can’t be around to observe, and it can only be seen in the fossil record. Another way to look at it is that “macro-evolution” is the accumulation of small changes or “micro-evolution” over geological time. If I start giving you a penny every year, that doesn’t seem like much money, but if I continue this for 10 million years, now you have $100,000.

One problem is trying to differentiate between what constitutes micro and macro evolution, which are essentially just terms people use to talk about the spectrum of change within a species. There is no quantifiable point where a change ceases to be micro and becomes macro, and there is no “force” allowing micro changes to happen but somehow stopping macro changes from happening.

Myth 6: Evolution is just a theory, not a fact
The word theory is used different in the sciences than in common parlance. When used outside the sciences, a theory is often taken to be little more than a guess, even if an educated guess. In the sciences, a theory is essentially an explanation for all the evidence that can be used to make predictions and retrodictions (i.e., it allows one to proposes falsifiable hypotheses that can be experimentally tested). Therefore, the success of a theory is not so much in how well it explains the available data; this is a prerequisite for a good candidate theory, but it is not sufficient, since such an explanation is underdetermiend by the evidence. Where a candidate theory goes from being just one of a set of possible good explanations to an actual theory (in the scientific sense) is when it can make accurate predictions and retrodictions that are confirmed through experiment. There is more subtlety to all this (see, for instance, verificationism; Karl Popper and falsifiability; Thomas Kuhn and paradigm shifts), but what I’ve said here is a good working definition of a scientific theory that illustrates how it is used differently by scientists and in everyday conversation. For more on facts and theories in the scientific sense, see my post dedicated to the subject here.

Myth 7: Evolution entails eugenics
Eugenics is the notion that certain human traits are desirable while others are undesirable, and so humans ought to promote reproduction between those who possess the desirable traits and disincentivize, or even outright prevent, reproduction between those with undesirable traits. Through such a program humankind can be made “better” by some metric. This was a popular idea in the late nineteenth and early twentieth century, though the Nazi eugenics program largely discredited it. There is still a line of thinking that the truth of evolution would entail eugenics – this is both by those who want to state this as a way of discrediting evolution, and by those who are proponents of eugenics. But this is a naturalistic fallacy, attempting to get an ought from an is: saying that because it is the case that evolution is true, then it ought to be the case that humans engage in eugenics programs.

Or, put in the form of a syllogism, the opponent of evolution might say:

if evolution is true, then humans ought to employ eugenics
humans ought not employ eugenics
therefore evolution is not true

Or, the the proponent of eugenics might say:

if evolution is true, then humans ought to employ eugenics
evolution is true
therefore humans ought to employ eugenics

But the ought does not follow from the is, just as nothing about the truth of the theory of general relativity entails that we ought to throw people off building roofs or put them into free-falling elevators. Furthermore, the idea of making humans “better” is, as we’ve seen, incoherent in an evolutionary sense; our notion of “better” would be subjective (e.g., humans value something like physical strength, and so making the average human able to lift a greater amount of weight would be “better” by some human standard, but not necessarily having greater biological fitness). Also, if we are to make a purely biological argument in terms of the survival of the human species, then it would be “better” to have more genetic variability, i.e., it would be a greater guarantee of humanity’s continued survival if we did not breed humans to have a narrower set of so-called “desirable” traits, and therefore if we value the survival of humankind, then we ought to maintain in our gene pool the traits that might appear “undesirable” by some subjective metric.

Now I’m going to talk about things a bit more abstractly.

Evolution is a Game of Economics

To think about this on a more abstract level, one has to remember that a beneficial trait has to have a cost/benefit analysis (by means of natural selection). Thinking about humans, the reason we do not have supercomputer brains is because it would not be economical on in an evolutionary sense. We would require bigger heads to fit bigger brains which a) would be more difficult to fit through the birth canal, b) would require more neck strength and skull protection (more ‘recourses’ would need to go towards making the bones and muscles in the head and neck stronger) and c) the brains we have are already energy black holes (just our brain uses about 20%~ of the total energy we consume).

So, essentially, natural selection has to do the equation:
[Beneficial trait] – [Cost in resources] = [Total overall benefit]

If the energy cost of having a larger brain outweighed the benefit of having a larger brain, it would make the trait ultimately less beneficial; the person with the smaller brain would actually survive better if, perhaps, there was a food shortage. The person with the large brain would require a lot more food to support the energy needs of the larger brain and the nutrients required for the stronger skull and neck muscles/bones. The selection pressure of a food shortage, or a disease (which would be taxing on the bodies energy), or one had to escape other dangers (being faster or stronger also requires energy), and the limiting factor of the birth canal size all prevent larger brains from becoming a predominant trait.

This can apply to other organisms, as well. Elephants do not become perpetually larger, even though their size make them better able to survive predation from lions. The increase in size would come with an increased need for food as well as oxygen.

In short, natural selection makes sure that organisms stay at a tenuous ‘balance’ by forcing populations to continually adapt to selection pressures, while at the same time remaining efficient.

Evolution Is A “Messy” Process

One aspect of evolution, which I just want to mention is that evolution can only “work with” what is already there. This is why we have vestigial organs (wisdom teeth, tail bone, etc) and suboptimal traits. Suboptimal traits are the reason humans get bad backs and knees – humans only recently (in evolutionary time) evolved to be bipedal, and we had to evolve this from being quadrupedal. A suboptimal trait is also why we can swallow water down our wind pipe, because the way our esophagus and trachea are arranged is not optimal.

As can be seen, the Esophagus and Trachea are ‘criss-crossed’ when it comes to breathing through the nose. Evolution “built” (for lack of a better word) the trachea this way when fish first began evolving what would later become lungs. Then later, noses evolved on top of that. In evolution, things are simply “built” on top of each other.

Concluding Remarks

That the diversity of life on planet earth came about as a result of evolution by natural selection is a fact. As we’ll see in part 2, the evidence for this is overwhelming. And, as we’ll see in part 3, biologists are not concerned with “proving” the truth of evolution. They have moved on to bigger things in the realm of evolutionary theory such as mechanisms, processes, occurrences, interpretations, explanations, mathematical rigor, and other higher concepts. What I’ve described in this post is the simple, elegant process by which evolution by natural selection proceeds. Within the scientific community, little if anything in this post would be considered controversial.