Evolution is an idea. A theory. An inevitability of infinite three dimensional space. Evolution is not Darwin, nor Dawkins, nor that biology professor that made the entire class buy his buddy’s book, making it a bestseller.
It is genetic, philosophical, and mathematical. It is a cornerstone of biology and the basis of modern medicine. The best possible explanation of the facts, though not the only explanation. Whether you agree wholeheartedly with the theory or treat it with disdain, I only ask that you appreciate the idea for the wonder it provides.
The Basics of Adaptation
Two deer butt heads for hours in an effort to win the affections of a waiting female. Again and again, they ram their skulls into each other, attempting to beat their opponent into submission. Eventually, one deer collapses and the other is victorious.
The match is close, but what neither of them know is that the winning deer had a slightly thicker ridge of bone on its forehead. Not by much- maybe a few millimetres, but in a contest this even it is what made the difference.
The deer’s children also possess this advantage, and they go on to win fights and have females fawn over them. Because the deer with thicker foreheads usually win, over generations, every deer will have a thicker forehead because the ones that don’t lose every fight, and are unable to have children. They are weaned out of the population.
Now out of these new deer, one has an even thicker ridge. The cycle is repeated, and after another series of generations all the deer have noticeably larger foreheads. Maybe a centimetre larger than before.
Two deer fight for a female
After thousands of generations, all of the deer have skull bones that stretch for a metre or more. The ones that have even slightly smaller antlers are at a distinct disadvantage, and they are cast aside.
This is what natural selection is- when nature selects the best and allows them to live and/or have more children. It is Charles Darwin’s great contribution to mankind, because it explains the differences between every living thing on the planet.
The idea is that there are always going to be more children than the surrounding environment can support. As a result, only the strongest children are going to survive. Nature is the closest contest there is, so even the smallest advantage is going to have an effect. Over millions of years, these advantages become established traits- the long beaks of toucans, the shells of snails, the claws of jungle cats. Every single trait has been selected for in a similar manner to the antlers of a deer, with no exceptions.
The mechanics of this selection, however, can be quite diverse. For example, a deer can be the fastest deer alive, able to outrun any predator. This is good, except that it has absolutely nothing to do with attracting a mate, or having children, which means that the deer’s speed will not be passed down to the next generation.
Similarly, a deer can have the largest antlers and be able to win every fight. But if it cannot run away from predators, it will not live to see those fights. In order for natural selection to work, an organism must survive until maturity and then pass on their genes to the next generation. Anything that helps any part of that process is an advantageous trait.
Beneath the Surface- Genetics and Microbiology
This is where Darwin’s part in the story ends. Surprising, maybe- the theory of evolution is largely attributed to him. But the fun stuff began when biologists began looking closer at what actually gave rise to new traits.
Imagine you have a spade, a flat square of metal attached to a wooden pole. You put the spade in a room with a monkey and a bunch of tools. That monkey is probably not going to do anything to the spade, most likely choosing to mess around with the tools and throw feces everywhere. Even if it does choose to work on the spade, it will probably destroy it, perhaps detaching the end or splitting the handle in half.
But if you repeated this a million times, one of them might take a hammer to the spade, bending the metal square into a U. The extremely unlikely result is a crude shovel, and you are left with a tool that was slightly better than before.
This is a variation of the famous monkey-typewriter thought experiment, where if you have an infinite number of monkeys randomly pressing keys on an infinite number of typewriters, within a day you will have the complete works of Shakespeare (you would actually have everything ever written and is ever going to be written). The same result would occur if you gave one monkey/typewriter combo an infinite amount of time.
Each monkey randomly hits keys on a typewriter
This is what nature does- throwing trillions of DNA codes into a room with a monkey and a toolkit, and sifting out the rare, improved proteins. The deformed proteins will result in an animal that is ill equipped to survive, and it does not get passed on for that reason, while the improved proteins will get passed on. The only criteria is that the improved protein must confer a survival or mating advantage.
Everything in an organism is regulated and constructed by proteins, which are essentially tiny, three dimensional machines. The cells of every living thing make these proteins from instructions in the form of a DNA code.
Basically, cells read DNA and use it as instructions to line up chains of amino acids. These amino acid chains start folding into proteins, based on the order of their arrangement. Even though there are only 20 amino acids (for humans), there are an infinite number of combinations and therefore an infinite number of shapes that proteins can take.
Every functional protein is simply extraordinary. They are the tiniest machines in existence, resembling channels, scaffolds, carriers for specific molecules, and much more. Some of them are motors. Every cell has thousands of different proteins, all fulfilling different functions. And every cell is more complicated than the most complex machine we humans have ever built.
This is a protein called ATPase, found in many living things, responsible for providing the cell with energy. It is also one of the smallest known motors
Take hair colour, for example, which is determined by three different pigments: black eumelanin, brown eumelanin, and pheomelanin (which is responsible for orange/yellow). Each of these pigments is a protein, and different combinations give the different hair colours we see, similar to mixing paints. These pigment proteins are built by cells according to instructions provided by DNA.
So someone with blonde hair would have a defective gene for both black and brown eumelanin (the protein product does not form properly and is destroyed), but a functional pheomelanin gene. Brown hair could have functional genes for brown eumelanin and pheomelanin, but not black eumelanin. The point is, it is not the gene that directly determines hair colour, it is the protein that the gene codes for. It is also possible to produce varying amounts of each pigment, another important facet of evolution. Sometimes, producing more or less of a certain protein can be an advantage.
The mechanisms of something as simple as hair colour can be immensely complex
But what happens if the DNA code for a protein is changed, or mutated? That would result in a different chain of amino acids, which would fold into a different protein. Most of the time, when this happens, the protein is less effective. Occasionally it is ever so slightly better.
We go Deeper- Genetics on Steroids
There are a number of problems with the random mutation mechanism. It is horribly inefficient, resulting in the crippling of an organism more often than an improvement, and absolutely nothing more often than that.
Furthermore, most of our genes can’t be mutated. We share many of the same genes and proteins as other organisms (you may have heard of some of these stats- how we are 96% similar to chimpanzees, 67% similar to mice, 60% similar to fruit flies. Note that these numbers come from bogus sources, but the point is that there is a lot of overlap).
These proteins are evolutionarily conserved, meaning that no matter how many generations pass they will remain more or less the same, having achieved maximum efficiency for their purpose. If you gave a Ferrari to a monkey, it will probably never improve upon the design. This is true across species– many of the genes for metabolism are the same in plants, insects, and humans.
One method of evolution is gene duplication and redundancy. A DNA code can be copied, and the result is two codes that make the same protein. Because one copy is more than enough, the other can safely mutate as it pleases without disrupting the organism. So instead of needlessly ruining the blueprints for the latest Ferrari, one copy is retained and used to build Ferraris while an extra is given to the monkeys.
Janus A got copied and changed slightly, into janus B, around 35 million years ago. Then around 10 million years ago, janus B got copied again and mutated into ocnus
Proteins can also have different sections, or domains, which form distinct shapes. For example, a protein could consist of a cube attached to a sphere attached to a pyramid, which all form separately from each other yet are still part of the same protein. Through various mechanisms (such as short DNA segments called transposons, that jump around, and recombination), these subsections can be cut up and glued onto other proteins.
This is like giving your monkey a spade and a knife, and your monkey removing the spade blade and attaching the knife to the handle, making a spear. The hybrid protein could perform a completely different function than before, but still use existing protein structures.
These two mechanisms are much more likely to result in improvements than random mutations. In fact, when we compare proteins from different organisms, we can see that some of them share domains (such as the zinc finger).
In reality, adaptation is a mixture of all these processes. A highly conserved gene can be copied, and then the copy can be cut up and glued onto other redundant copies, then mutate randomly to form a super protein that either replaces an existing one, or performs an entirely new function altogether.
Human Evolution
Little novel changes do not have a visible effect for thousands of generations. But they do have an effect, and we can see some of these in humans. Lactase, an enzyme which helps digest the lactose in milk (not having it means that one is lactose intolerant), normally phases out by adulthood. Yet, a few individuals in Europe and Africa had the ability to digest lactose throughout their lives.
Until the domestication of cows and goats, this ability did not mean much- whether a human being survived or died did not depend on the ability to drink milk as an adult. But after cows were regularly domesticated, being able to digest milk became a massive boon during tough winters, which meant that people who could had a distinct survival advantage. Over many generations, more and more people had the ability (because the ones who didn’t died more often). This is why many East Asian populations are lactose intolerant- being able to digest milk was not necessary to survival.
Speciation
Believe it or not, everything we have discussed so far is science that has been established for decades. And a succinct summary at that- traits are not usually determined by one or two proteins, but hundreds, all working in concert. Proteins from one cell can move across the body and then set off a chain reaction involving millions of proteins, sugars, and fats from billions of different cells. The hair example discussed earlier is not even properly fleshed out- there is still much we have to learn about the genetics of hair colour, and that is an absurdly simple case when compared to some of our hormonal processes.
However, a key component of evolution is the ability of organisms to adapt so much that they become new species. This happens when two or more groups are separated and placed in different environments.
For example, polar bears evolved from brown bears that are thought to have migrated north, and then were trapped by an ill timed glaciation event. Conditions were harsh, and only the biggest, strongest brown bears survived, the ones possessing the proper protein mutations. Lighter fur (the lack of pigment) was an advantage for hunting, allowing the bears to blend in with the snow and ice.
A mark of speciation is that the new species eventually become unable to mate with the old. Polar bears are still able to mate with brown bears- evidence that they diverged from brown bears relatively recently.
Yet many similar species are not able to interbreed. What determines where the line is drawn?
To answer that, we must go back to genetics. When the sperm meets the egg, they must be genetically similar, or the fertilized egg will die. If two groups are separated for enough generations, the sperm from one group will be incompatible with the egg from the other group. This is because the development of an embryo is mediated by proteins! If the proteins are too different (they have mutated too much, or acquired new characteristics), the embryo will notice something wrong and the pregnancy will terminate.
This is also why some species can still interbreed. Polar bears and brown bears still have enough of the same embryonic proteins, so the sperm and the egg can still work together to form a functional embryo. This also applies to humans- even though humans come in all different shapes, sizes, and colours, we did not diverge long enough ago to become incompatible with one another.
Sources:
Image of deer fight retrieved from http://news.bbc.co.uk/media/images/46583000/jpg/_46583676_fight4.jpg
Image of monkey typewriters retrieved from http://www.bersin.com/blog/image.axd?picture=monkeyfinal_1224016198.jpg
Image of ATPase retrieved from http://palaeos.com/bacteria/glossary/images/F_ATPase.gif
Image of hair pigment retrieved from http://www.nature.com/hdy/journal/v97/n3/images/6800861f2.jpg
Image of duplication and divergence retrieved from http://www.nature.com/nrg/journal/v8/n9/images/nrg2167-i1.jpg
Surreal Science Stuff 
