On Evolution by Natural Selection

By Jacob L. Fine

“It’s only a theory!” Heard it before? Like many words in the English language, the word theory has evolved different meanings. Our daily use of the word theory is not in any way related to how the word is used in science. In the context of physics, chemistry and biology, the word theory came to denote any highly verified and predictive explanation for an interconnected body of facts. There is the theory of gravity, the germ theory of disease, the theory of continental drift, the atomic theory and more. Theories explain facts. In biology, the theory of natural selection explains the fact of evolution. Biology cannot truly be understood without it.

Before we describe the theory of evolution, let’s distinguish this from the fact of evolution. Natural selection explains the fact of evolution in the same way that Newton’s laws of motion explain the fact of motion. Still, both explanations are technically theories using the scientific definition. At any point in time, there exists an optimal explanation for all of the current known facts. That optimal explanation is exactly what a theory is. Currently, the optimal explanation for the fact of evolution is the theory of natural selection. For a more comprehensive look at how theories work, please refer to this article about the scientific method.

No sincere scientist disputes the claim that “there was evolution.” All physical things joined the causal network of the evolving universe at some point after the Big Bang, some 13.8 billion years ago. The complex universe we live in today didn’t just emerge fully formed, rather, it came together bit by bit as an accretion of origins kicked off by the Big Bang. The origin of life is one such event, which occurred approximately 3.5 billion years ago. The causal network of the evolving universe includes origins of all kinds, at measurable times, from bacteria to eukaryotes to fish to plants to amphibians to reptiles to dinosaurs to birds to primates to hominins to humans. The current state of the universe is the sum total of all origins, starting 13.8 billion years ago.

We can now look back at all kinds of origins (not just biological) from the internet (~29 y.a.) to the printing press (~580 y.a.) to wheels (~5500 y.a.) to agriculture (~10,000 y.a.) to the end of the most recent Ice Age (~11,700 y.a.) to cave art (~14,000 – 40,000 y.a.) to the first dogs (~15,000 – 40,000 y.a.) various human migrations from Africa (~60,000 – 70,000 y.a.) to language use (~50,000 – 150,000 y.a.) to Neanderthals (~40,000 – 130,000 y.a.) to early humans (~200,000 – 300,000 y.a.) to Homo heidelbergensis (~300,000 – 700,000 y.a.) the use of fire by Homo erectus (~1,500,000 y.a.) to the common ancestor of humans and chimpanzees (~6,000,000 – 7,000,000 y.a.) to the last dinosaurs (~65,000,000 y.a.) to the first living things (~3,500,000,000 y.a.) to planet earth (~4,500,000,000 y.a.) to the entire universe (~13,800,000,000 y.a.). Obviously, plotting the origin of everything as a function of time would take light years of paper, but the message here is clear: all physical things originated at some point in the grand causal network of the evolving universe.

A variety of methods exist to date some of these distant events including relative dating, radioisotope decay, and paleomagnetism. Explaining each of these methods would take pages, so if you’re interested in learning more please follow this link. The main thing to take away from geological dating is the fact that independent measurements by different scientists all tell the same story. If these methods are applied consistently across all accurately measured fossils, a beautiful sequence of change with time can be established, all going back to the origin of life. This is only one of many ways the fact of evolution is confirmed.

To understand how evolution occurs in biological systems, understanding the idea of natural selection is essential. In a very basic sense, natural selection explains how life gradually and incrementally adapts to the environment by acquiring small heritable changes. Genetic changes that occur in germ cells (in humans, germ cells are eggs or sperm) are passed on to future generations. If any change increases the number of offspring an organism can have, then such changes are likely to become more common in a population. If an increasing number of tiny changes occur in some lineage, then that lineage could become vastly different.

In a population of varying organisms, this variation is always acted upon by an “invisible hand” which Darwin called natural selection. This natural force generates a “tendency for varieties to depart indefinitely from the original type,” (the name of an article on natural selection by Alfred Russel Wallace) which wholly summarizes the theory of evolution by natural selection. This means that any change which improves replicative ability will become more common, no matter how slight. This elegant and simple idea can in part explain how eyes evolved from eyespots, brains from nervous tissue, multi-cells from uni-cells, and so on. If microevolution is repeatedly iterated on a population such that small changes slowly accumulate over many generations, macroevolution occurs. In these conditions, the summation of microevolution is macroevolution. But how can tiny changes produce vast differences? To answer this question one needs a basic understanding of genes.

Genes are like ingredients that make organisms. Changing the genes may change the organism drastically, minutely, or not at all. Sometimes, extremely tiny changes in genes can produce catastrophic downstream effects in the organisms they build. For instance, one difference between chimps and humans is the genes involved in the number of rounds our neurons divide. The quantity of neurons is one of the few things that separates us from other primates. Different expression in just a few human genes causes a domino effect leading to three times as many neurons as chimpanzees. The mere difference in number of neurons is one necessary reason why we have ideologies, languages, philosophies, religions, and political systems and chimps don’t, as explained by the leading neuroendocrinologist Dr. Robert Sapolsky in this video.

As a brief but relevant aside, for all 20,000 – 30,000 genes in humans, there exists a nearly identical “cousin” gene in chimps. Even the random genetic mistakes (repetitive DNA like telomeres, VNTRs, and transposons) are in the same exact relative positions! That’s like finding two slightly different copies of an ancient book with the same exact typos in the same exact places! If you compare the DNA of any very closely related organisms, you’ll find the same exact thing: the “typos” are in the same places. The chances of those same exact typos arising without common descent is simply impossible.  

The idea of downstream amplification is important for evolution to work. Fortunately, much of biology is all about downstream amplifications: one miniscule change often leads to a cascade of results. As the effects of miniscule changes multiply down the “stream” of causation, there could be catastrophic differences. For instance, the difference between someone who has sickle-cell anemia and someone who doesn’t is one single amino acid in the hemoglobin gene. The difference between colour-blindness and normal vision is a small change in any one of the SWS, MWS, and LWS (short, medium and long wave sensitive) opsin genes. Microcephaly, or “small head” is a disorder that can be caused by mutations in the ASPM gene, as discussed on this NIH webpage.  

It’s possible for small changes to produce vastly different outcomes in a single organism. We also know that ancestors are not identical to their offspring; in fact, they might even differ drastically within just a few generations. Look at savants; people with extreme abilities in some areas are extremely rare, but do occur in 0.0001% of the population.

Some well-known savants include Stephen Wiltshire and Kim Peek. Did the near ancestors of Stephen Wiltshire draw complete landscapes in full detail based only on memory? Could the near ancestors of Kim Peek speed read both pages of an open book at once and retain 98% of the information? Clearly, we know it is possible for offspring to have drastic beneficial differences from their ancestors, even within a few short generations. As these drastic differences are iterated of multiple generations, even more drastic outcomes could result. Maybe something akin to this could in part explain how ape-like creatures evolved into humans over 7,000,000 years.

Since genes are far upstream in the chain of causation, tiny changes in genes (early on in development) can result in massive differences, which may either be beneficial or detrimental. Genes in general are involved in determining traits such as skull size, body mass, eye colour, hair colour, brain size, neuron functioning, bone density, height, number of fingers, number of wings, skin pigmentation, jaw shape, and so on. It is taught in first year genetics courses that changes in one or few genes could change entire organisms from tall to short, five-fingered to six-fingered, small-head to large-head, white-coat to brown-coat, blue-eyed to green-eyed, black hair to blonde hair, hairy to hairless, sighted to blind, healthy to diseased, long-beaked to short-beaked and so on. If any of these changes happen to suit the environment, the organism that has them will probably reproduce more. Within a shorter time than expected, these changes may become fixed in a population, in which every member is tall, five-fingered, small-headed, white-coated, blue-eyed, black-haired, hairy, sighted, healthy, long-beaked, or vice versa.  

Gene duplication also plays a major role in the evolution of new genetic information. When gene duplication occurs, an existing gene is copied and mutated in such a way that may or may not be advantageous. Based on the idea of natural selection, we know that all genes better at replicating themselves become more common. If a mutation coincidentally happens to be beneficial, then it automatically becomes more common. That’s in part how hemoglobin and myoglobin evolved from ancestral globin proteins. Also, trichromatic vision (seeing mixtures of red, green, and blue) most likely resulted from one gene duplication and mutation over the course of evolution. Many other traits evolved this way and for more information on them, please follow this link.

Sometimes nested in the process of selection is the tendency for complexity to increase as natural selection operates. It should be said here that evolution does not have a final goal or teleology. Natural selection doesn’t “forsee” the adaptive value of a trait in 1,000,000 years’ time. If the evolutionary tape were rewound and played again, there is almost no chance at all that things would be the way they are now. In this view, asking why humans exist is like asking why North America is shaped the way it is. Just as the continents happened to spread out in the way they did, so too did selective pressures happen to construct Homo sapiens and all other life forms.  

To the evolution skeptic, in spite of all the evidence, the mere idea that microbes could evolve into philosophers seems ludicrous. It’s crucial here to remember that we are talking about 3.5 billion years. That’s three and a half million one thousands! Keep in mind that it only takes nine months for tiny zygotes to develop into fully formed babies. It takes just another thirty years for zygotes to become presidents, doctors, dictators, bankers, scientists, and philosophers! From tiny seeds come forth giant trees.

Despite this analogy, evolution and development are two related but distinct processes. Explaining each and every evolutionary step from microbes to philosophers is immensely more challenging than explaining each and every developmental step from zygotes to presidents. Still, evolutionary and developmental models for many phenomena do exist and are continually being improved upon as more evidence becomes available. Just because we can’t show how something changed with time doesn’t mean it didn’t change with time. A good example is language use. Language use emerged in the causal network of the evolving universe at some point, probably 50,000 – 150,000 years ago. Though we don’t know exactly how it emerged, we know it did emerge and can approximate when.

It would be quite timely to discuss the evolution of hearts, eyes, lungs, kidneys, brains, wings, fingers, leaves, shells, teeth, stomachs, and intestines all in this article. But for the sake of time, we will discuss how natural selection can be applied to one of these supposedly “irreducibly complex” systems: the nucleus-containing cell, a.k.a. the eukaryote. The best model that explains how eukaryotes evolved is known as endosymbiotic theory. In Ontario, endosymbiotic theory is standard curriculum in high school biology (Figure 2).

1. The outer membrane of an ancestral “proto” eukaryote folded inward on itself many times to create little “bubbles” or vesicles that gradually piled up around the location of genetic material. This provided many advantages. For instance, the DNA became more “sealed-off” from other parts of the cell where more metabolic processes could occur. The “sealed-off” DNA eventually became the nucleus. Other “pinched-inward” parts of the membrane gradually evolved into the endoplasmic reticulum. These facts are confirmed by the observation that the nucleus is enclosed by a double-membrane structure (which makes sense for biochemical reasons) and the fact that inward-membrane-folding to form small “bubbles” happens all the time in modern eukaryotes.
2. Eventually, a small aerobic (oxygen compatible) bacterium was swallowed by this early cell. The main early-cell and the bacterial intruder provided each other with mutual metabolic benefits. Cell-eating (a.k.a. phagocytosis) happens all the time in modern eukaryotes. This aerobic bacteria evolved into modern day mitochondria. Evidence for this includes the fact that mitochondria have bacteria DNA, divide independently by binary fission (which is exactly how bacteria divide!), have very similar membrane components (proteins and sugar-fats), membrane processes as bacteria. They also have a double-membrane structure, which would make sense to the biochemist only if they were once swallowed up.
3. For some lineages of this proto-eukaryote, a photosynthetic bacterium (cyanobacterium) was swallowed in an analogous way. This is confirmed by similar reasoning.

It should be said that these three parts are only snip-its in the sum total of all events in the causal network of the evolving eukaryote. Sub-pathways such as the evolution of chromosomes, ribosomes (protein making machines), and membrane proteins had to happen alongside these three steps. They all joined the causal network of the evolving eukaryote at some point in time. Fortunately, plenty of models explain the evolution of these structures. The key takeaway is that it all happened gradually and incrementally, with proteins, genes, cells, and organisms slowly diversifying in structure and function.

A more fundamental and generalized definition of natural selection is this: things that are better at replicating become more common. This law applies to non-biological systems as well. In biology, replicating just happens to depend on having more offspring. Generalized natural selection acts on baby names, recipes, alphabets, languages, ideologies, internet memes, fashion icons, cell phones, magazine covers, and more. In a population of varying baby names, baby names that are more desirable become more common. As conditions change, different baby names may be less desirable and therefore become less common. The 6,500 complex languages and alphabets that exist today didn’t just pop into existence either, rather they too gradually and incrementally evolved from earlier languages and alphabets. A good example is how the modern English alphabet (a.k.a. the Modern Latin Script) evolved from earlier alphabets:

To reiterate, many complex things don’t just pop into existence fully formed. More often than not, they gradually and incrementally evolve. Stone axes lead to bronze axes, next iron axes, and ultimately the modern chain saw. Late Modern English language evolved from Early Modern English, which evolved from Middle English, which came from Old English, which emerged from even earlier languages. Before the PlayStation 4, there had to be a PS3, PS2, and the original PlayStation. Before the iPhone 11, intermediates from the iPhone 1 to the iPhone 4 and beyond survived and reproduced. Similarly, before Homo sapiens, there had to be Homo heidelbergensis, Homo erectus, Homo habilis, Paranthropus, Australopithecus africanus, Australopithecus afarensis, and dozens of other intermediate species found in the fossil record (Figures 4 and 5). But the iPhone 1 didn’t emerge fully formed either. Before the iPhone came flip phones descended from chord phones, before which came rotary phones. Likewise, before Australopithecus afarensis came earlier primates descended from even earlier organisms (Figures 4 and 5). The mechanisms of biological evolution are quite different from non-biological evolution, but the fact that both involve change with time, and the occasional increase in complexity is the same. To reiterate, biological evolution doesn’t necessarily make organisms “get better” like computers do, rather, it makes organisms more adapted to their specific environment. Since adaptiveness depends on the happenstance conditions of the environment, an adaptation today might be a non-adaptation tomorrow.

If you wind the evolutionary tree of life back enough, you’ll get to the origin of all life some 3.5 billion years ago. What caused that? The short answer is “we don’t know,” but some primordial soup of interacting chemicals is plausible for the biochemist. Darwin explained the origin of species. As for explaining the origin of life, diligent scientists are working on it as we speak.