Cognitive Science: An Introduction/What is evolution?

Evolution is when things change incrementally over time. In this sense, the smartphones evolve because previous smartphones look slightly different from the ones that came before them. But most of the time, when people use the term "evolution," they mean that the changes are happening due to some selection process. In biology, this is evolution "by natural selection." Indeed, unless mentioned otherwise, in this book the term "evolution" will refer to evolution due to some kind of selection process (be it natural, artificial, or sexual.)

Although the concept originated in biology, and that remains the primary focus, evolution seems to be a widespread phenomenon. Philosopher Daniel Dennett calls it a "universal solvent" because of its ability to help us understand so many things.

Anyway, here is the basic idea...

How Evolution Works
Evolution will happen whenever these conditions are met:


 * 1) There is a population of entities that show some variation.
 * 2) Those entities can get copied (either by themselves or by something else).
 * 3) Those copies maintain some attributes of their "parents."
 * 4) Some entities are more likely to get copied than others.

And that's it! Any system with these traits will undergo evolution, be it jokes, a species of frog, or virtual creatures simulated on a computer.

Here's how it works.

tk describe how evolution works in a basic way

Variation
Evolution requires a population of entities that show variation. This means that they are not all the same.

Mutation
In entities with DNA, some of the variation is due to something called mutation. Each living thing begins as a single cell, with a single set of DNA. This might get mutated if it is hit with a cosmic ray, changing the code very slightly. DNA can also be changed by copying errors. When cells split, they have to copy the DNA. Although there are mechanisms in place for error-correction, sometimes mistakes get through anyway. The earlier this happens in development, the more cells are affected, because the error is replicated into all of the cells created from that cell with the DNA. These are point mutations. Many such changes will have no effect on any traits that might influence selection, because about 97% of the genome is non-functional. But once in a while, it will have some effect, usually with a detrimental effect.

Sometimes mutations are more drastic. During replication, long segments of DNA might be duplicated or removed. These are much harder to correct, and are more likely to affect traits of the individual.

The most large-scale mutation is when an entire chromosome is missing, or an additional one is added. For sexually-reproducing creatures, each cell has two copies of each chromosome: one from the father and one from the mother. The exception is the mother's egg and the father's sperm, which only have one copy each. When the sperm fertilizes the egg, you get a cell with two copies of each chromosome. But sometimes an error happens, and one chromosome is left out or an extra is added, so that the resulting cell only has one copy, or perhaps three. This is often deadly, because with only one copy the cell will only make 50% of the proteins it's supposed to, and with an extra copy it will make 150%.

Sexual Reproduction
For asexually-reproducing species, each offspring has the same genes as the parent, aside form copying errors. In sexually-reproducing species, however, each child gets half of their genes from the mother and half from the father. This recombination is a major source of variation.

Half of an organism's genes come from the mother and half from the father. What these genes are depends on which genes are in the egg and sperm cells that come together for fertilization. Each has half the number of genes as the parent. These sperm and egg cells, however, come from parents who have a full genome. When a sperm or egg cell is created, it mixes and matches the genes of the parent, in a process called crossover, which is another major source of variation.

Where do New Genes Come From?
Different organisms have different numbers of genes. Mutation explains how genes can change over time, but where do new genes come from?

Sometimes a physical gene will get duplicated due to a copying error, and then the offspring have one more copy of a gene. At first, this gene will code for the same protein (assuming it is a functional gene), but over time it will mutate on its own. That is, the two copies will mutate independently. Over time, one might mutate to code for a new protein.

Selection
The individuals who reproduce and pass on heritable traits are those considered selected. Suppose a moth with a splotchy colouration survives better on trees because of local pollution. This splotchy colour is considered a phenotype, which is the manifestation of some heritable trait in the world. The underlying code that generates the phenotype, in living things, is called the genotype. Selection can refer to either the phenotype or the genotype.

Usually, we think of selection happening because the phenotype allows the individuals to better reproduce than those without it. This is classic selection. The basic categories of selection include natural, sexual, and artificial.

Natural Selection
Evolution by natural selection theorizes that the natural genetic variation within species would yield survival advantages for some and disadvantages for others. Those phenotypes that yielded survival benefits would be more likely to pass on to offspring, increasing its representation in the gene pool, to eventually encompass the entire species.

What is a gene?: You might be surprised to hear that the term gene is used in many ways, even in science. Which meaning is intended has to be figured out from the context. Here are a few of the common meanings.

The Physical Gene: "Gene" might refer to a physical stretch of DNA that is used to create a single protein. In this sense, the gene for blue eyes in your liver cells is a different physical gene from the ones actually in your eyes.

The Informational Gene: A sequence of nucleotides that describes not only one physical gene, but every instance of the same sequence in every other physical gene that has ever, will ever, or could ever exist. This is the sense of gene we use when we say that you have one of your mother's genes. You obviously don't have her physical genes.

The Hereditary Gene: "Gene" might refer to a unit of heredity, like blue eyes. This might be caused by a complex of informational genes across a population. There might be several informational genes that result in the same hereditary gene. Different genetic variants might all cause red hair, for example.

Sexual Selection
A form of natural selection is sexual selection, and acts on the mating of amphimixis organisms - those who engage in sexual reproduction. Sexual selection acts by favoring traits or behaviors that enhance an organism’s reproductive advantage. It selects for traits and behaviours that increase the probability of successful reproduction. This is how sexual selection differs from natural selection, which selects for traits and behaviours that confer advantages on survival. Some traits that are sexually selected for may actually decrease and organism’s survival potential. Hence, some traits favoured by sexual selection may be selected against by natural selection. A typical example of sexual selection involves a single female and several males competing to mate with her. Sometimes males fight or compete with each other for female mating opportunities (intrasexual selection), and sometimes females choose males based on their observable characteristics (intersexual selection). For example, the peahen will choose her peacock mate depending on the color of color of his feathers. Males with more blue-green in their eyespots achieved greater mating success.

Mechanism of sexual selection
Conspicuous traits, may at first glance appear to yield no fitness advantage, such as the extreme ornaments on ungulates, or the mating rituals of the bowerbirds emerged due to its ancestor’s matting selection. These sexual selection pressures can be classified into two subcategories: intrasexual competition and intersexual competition. Intrasexual competition occurs when members of the same sex compete. These competitions are physical or ritual displays of trait that portrays physical strength or vitality. One example is the males of the orange throat darter, who fight by flaring their fins, chasing, and/or biting. Similarly, humans males have been found to exhibit intrasexual competition by non-lethal wrestling for mating advantages while human females may use gossiping tactics.

Intersexual competition, or sometimes referred to as epigamic selection, occurs when one sex decides their mate based on their observable traits or behaviors. This type of competition is common in birds, where the female chooses the most flamboyant males by their feathers or singing. Birds-of-paradise have remarkably complex and diverse courtship displays where the female chooses from a selection of displaying males.

Precopulatory sexual selection occurs when the selection occurs before copulation, while selection that occurs after copulation is known as postcopulatory sexual selection. Postcopulatory selection was relatively unknown until 1970 when zoologist Geoff Parker introduced the world to the idea of sperm competition. Where non-consensual sex occurs in the animal kingdom, scenarios occur where after multiple male’s ejaculate competes to fertilize the female’s egg. In such cases a male can do nothing to increase their fertilization chances other than investing in larger sperm production or stopping future copulations. On the other hand, some females have ways of influencing which sperm fertilizes her egg. For example the female of Scatophaga stercoraria will displace unwanted male sperm and allows only that from her selected mate. Female mosquitos will resist to unwanted male by kicking them. House mice will deny future copulation efforts by using a copulatory plug made from coagulating proteins.

Which sex gets to choose?
While sexual selection is often portrayed as the female’s prerogative, there many species where it is the male who choses the mate. The male Jamaican field cricket chooses females based on their body size and mass. Male gulf pipefish prefer females within similar body shapes to theirs. The male killifish chose the largest available females to mate with. While more often it is the female of a species who chooses their mate, this is attributed to the difference in gametic investment. Males have a low-cost investment in producing sperm, while females have a higher cost of producing and incubating their egg to maturity.

Common factors come into play for some species, for example, mammals (except for the platypus and echidna) undergo internal pregnancy and give birth to live young. In this case a greater investment in energy is needed to nourish and protect the unborn fetus. This increased energy investment explains why female mammals tend to choose their mate. Intersexual competition within the human species can be culturally specific. A large study showed that human males tend to choose women with smaller feet sizes, except in a rural Indonesia, where they prefer females with the largest sizes. Males also have an innate preference for physical attractiveness, while women may be more interested in social status and resources.

Physical characteristics may be attributed to the good gene hypothesis, which states that mates are choosy towards those possessing indicators of genetic quality. Good genes do not only indicated by physical characteristics, but also by potential quality of parental care, economic status, or morality.

Whether intersexually or intrasexually, employing dating tactics to secure mates is commonplace throughout human civilization. Teenagers often employ denigrating gossip and rumours to devalue potential mating competitors. Clothing brand labelled have been seen by some scientists as signals of intrasexual competition. Emotional jealously can also play a factor in intrasexual competition, where strategies of exploitation and deception may be employed.

Problems with sexual selection
While sexual selection can lead to greater survival fitness within a population, it can also lead too the opposite result. The Fisher-Muller hypothesis states that by bringing beneficial mutations together allows natural selection to operate at a much quicker rate compared to asexual species. However it can also lead to a maladaptive process called the Fisherian runaway. Where one sex may prefer a trait of a potential mate, this preference may lead to both sexes developing a strong selection towards it. The choosy sex will then tend to select mates with the strongest expression of this trait. As each generation selects for the strongest expression, this trait becomes exorbitant displayed in a runaway expression-selection feedback loop. When a trait is expressed to the extreme it often requires a large amounts of energy and resources to maintain it. This potentially lowers a species’ chances of survival. When sexual selection is not pushed to the extremes, males who invest in high energy-consuming traits do not increase their survival chances. Referred to as the handicap principle these traits may slightly harm survival fitness while signalling reproductive strength and successful genes.

Artificial Selection
The process of artificial selection is defined as “a breeding process in which a population of organisms is screened for some quantitative trait or traits and those individuals rated highest are used as parents for the next generation.” In a letter written by renowned scientist Charles Darwin, he described how he discovered the theory of evolution through natural selection by stating he “came to the conclusion that selection was the principle of change from the study of domesticated productions; and then, reading Malthus, I saw at once how to apply this principle.” Darwin divided up selection into three categories: natural, methodical, and unconscious selection. Methodical selection is when humans choose organisms/animals, take them out of their familiar surroundings, and place them in unfamiliar habitats in order to preserve and enhance the gene pool. Unconscious selection is where humans artificially select the organism without the intent or knowledge of its long term effects. Methodical and unconscious selection are the original Darwinian principles that comprise artificial selection, which continues to have a significant impact on today’s world.

Darwin’s Galápagos Islands We have learned a lot about artificial selection in the past century, and the theory of selective breeding was first introduced by world-renowned scientist Charles Darwin. Through thorough research and understanding, he realized that the finches on each island were similar but different species. The unique species of finches have adapted to their climate on their specific island. In the past few decades, ever since the discovery of these rare species of birds, which was the first stepping stone to the theory of artificial selection, tourism has gone up. Everyone loves the opportunity to look at things they’ve never seen before, which is great for the tourism business, however, there are consequences of human travel. Over the last few decades, the effects of mass human exposure have been drastic, changing the overall environment and its species. A study concluded that the gut bacterial structure of the birds with heavy human presence was different from the ones with lower human presence. With medium-sized finches, their bacterial diversity levels were lower where they had a human presence compared to finches without human presence. Scientists also discovered invasive plants, also known as alien plants, which are impacting biodiversity on the islands. Of the 370 plant species, sixteen percent of them are alien plants. Studies also show that the alien flora will find ways to naturalize on the islands while the human population booms through tourism. Human exposure has affected the natural landscape and its species, which is a result of one of Darwin’s breeding principles, the unconscious selection.

Plant Breeding Another example of artificial selection is plant breeding. Plant breeding is the process of changing plant traits to develop new phenotypes and desired characteristics. The first genetic modification of plants dates back to almost 10,000 years ago, and the technological advancements used to genetically modify plants have only gotten better. Scientists use genetic modification methods to manipulate the genetic identity of these plants and tailor their specific functional requirements. For the most part, genetic modification has been beneficial for agriculture. For instance, according to the Introduction to Plant Breeding, oilseed and cereal crop production has drastically gone up since the ‘baby boom’ era, as have the production of fruit, vegetable, pulses, and root crops. These high increases have been a result of “heterotic advantage of single crosses over homozygous inbred lines.” Plant breeding does, however, come with its fair share of problems. In the Journal of the American College of Nutrition, there was a study done comparing the nutritional values of genetically modified foods. They found levels of decrease in thirteen important nutrients in their garden crops, including protein, calcium, phosphorus, iron, and many more. Though this study is dated, it is hard to imagine any drastic changes in these findings especially considering that scientists continue to genetically modify food sources. The methodical selection of plant breeding has been, for the most part, successful in modifying plant genetics, however, the process of plant breeding has not yet been perfected.

Selective Breeding in Farm Animals Animal selective breeding is the principle application of genetics to enhance the efficiency and production of animals (mostly farm animals). Over the last sixty years, meat and egg production, milk yield, and the growth rate of animals have all increased due to selective breeding. According to an article by two researchers, genetic selection can help “alleviate welfare problems in farm animals. This can be done by direct selection against undesired behaviors, such as aggression in pigs or feather pecking in laying hens.” Welfare problems, such as beating and dragging animals, will result in a reduction of both the quality and quantity of food and future offspring. Scientists are also figuring out ways to incorporate multiple goals in future breeding programs. These goals include chicken meat that is environmentally stable, and using birds with lower disease levels without the need for medical attention. Of course there are always cons that come with the pros. For instance, with the increase in milk yield, it has also caused a decline in fertility rates and increasing leg and metabolic issues. There is also a correlation between increased milk yield and genetic deterioration. Overall there have been many technological advancements in animal selective breeding, however, there are issues that need to be fixed for it to be perfect.

Main Artificial Selection Effects Although there are many benefits to artificial selection, there are many negative factors that come into play. The artificial propagation of species can also accidentally select for and spread maladaptive characteristics in wild populations. If the animals with maladaptive traits start breeding with wild animals, these traits could spread throughout the whole area, which will likely affect the animals’ productivity. In a study conducted on mice in early 2020, they took ‘high running’ mice that were successfully bred through seventy-four generations and four mice that were not used to wheel running. At the end of the time period, the mice that were bred from healthy parents had a better digestive tract; this is a result of “locomotor activity, body composition, and/or food consumption.” Research also shows that generations of healthy, active offspring tend to be in better shape both mentally and physically compared to others.

Conclusion Through the ideas and research conducted by the late Charles Darwin, he has identified the principles of artificial selection: methodical, and unconscious selection. Using his theory, scientists in today's time have utilized his research to perform genetic mutations in animals and plants to improve their characteristics. Although their experiments have been mostly successful, there are still issues at hand that need to be solved, such as the spreading of maladaptive traits, loss of nutrients in essential foods, and many more. To conclude, methodical and unconscious selection are the original Darwinian principles that comprise artificial selection, which continues to have a significant impact on today’s world.

Exaptation
Exaptation is when a phenotype evolved for one thing eventually gets used by evolution for something else. It is also known as preadaptation or coadaptation.

Examples are numerous, because just about every phenotype we see in contemporary life is exapted. Your arms used to be fins, your ear bones used to be jaw bones back when our ancestors were reptiles.

Introduction
Exaptation is defined as the co-optation of a trait for a new function that differs from the function it originally had. The term was coined in 1982 by Gould and Vrba when they noticed a tendency for organisms to have features that enhance fitness but were initially naturally selected for a function differing from their apparent current use. ; . Later, Gould showed that exaptations are not rare occurrences, but prominent features of evolution ; But neo-Darwinian theorists at the time largely ignored the idea of exaptations in evolution because their theories on evolution revolved around being heavily adaptation centric ;. They believed that every trait is an adaptation that enhances fitness and was directly selected for by natural selection. However, the evidence supporting exaptations that Gould and Vrba demonstrated was convincing and quickly changed the field of evolutionary biology.

While there are countless examples of exaptation in biology, use of the term in more recent years has been declining relative to the use of the term ‘adaptation’. Lack of a formal definition for exaptation that distinctly differentiates it from adaptation has been attributed to the failure of exaptation to be used more often in evolutionary biology. Instead, the term exaptation has found a home in studies of technological innovation. Since selection in biological evolution is usually blind – meaning selection occurs on traits being acted upon by multiple environmental pressures without forethought – but technological evolution is usually guided or directed with forethought, it is significantly simpler to elucidate the original function of a technological trait than of a biological one. Thus, it is much easier to determine when the current function of a technological trait is exapted from its original function. In this sense, the field of technological innovation has exapted the term exaptation from evolutionary biology.

Biological Exaptations
Biological exaptations are features that an organism has that initially serve one, or sometimes no, purpose, but later begin to serve a different purpose. A classic example of biological exaptations is feathers on most modern birds. An ancestor of modern birds, Archaeopteryx, is the first known organism to have had feathers for flight, although it was likely only capable of very simple flight. ; . Other feathered dinosaurs used feathers for their original adaptation: insulation. Thus, Archaeopteryx exapted feathers for a different purpose (flight) from the purpose they originally served (insulation). Many examples of macroscopic exaptations exist. A study by Konorov et al. provides evidence to suggest that the black garden ant, Lasius niger, has genomic exaptations that help it to thrive in urban environments. These ants have increased pollutant resistance due to coevolution with parasitic fungi, which has been exapted to aid them in dealing with pollutants present in urban environments. Genes of odorant receptors and odorant-binding proteins are less abundant in L. niger compared to other ant species. It is hypothesized that this species underwent this gene loss because of their transition to a terrestrial lifestyle where visual information and antennal contact is a significant part of their communication. Regardless, odorant receptor loss is an exaptation for urban environments because it increases the ants’ resistance to repellants and decreases their reliance on pheromones which can be easily concealed in urban environments.

Examples of biological exaptations are shown from the molecular scale as well. The understanding of transposed elements, repetitive DNA sequences formally considered selfish DNA, has expanded because of the concept of exaptation and its adoption in molecular genetic research. Transposed (or transposable) elements are now known to undergo transposable element exaptation, which helps maintain the structure of the genome and to create variation within it. Transposable element exaptation is a process where transposable elements become novel host genes instead of simply replicating themselves in the genome. These new host genes can have phenotypic benefits and can contribute to genome evolution. The act of transposable elements creating new genes which become exapted by the organism is involved in the evolution of many physical traits.

Technological Exaptations
Shortly after the term exaptation was added to the evolutionary biologist’s vocabulary, scholars interested in innovation and technological changes appreciated the value of the term for their own vocabularies. It has since been theorized that exaptation is more commonly used and important to technology historians and similar scholars than to biologists and other natural scientists.

In 1966, Corning, an American glass company, learned of the ongoing work in fiber optics. The company decided to investigate the potential of optical glass fibers and, using their expertise in glass production, created glass optical fibers useful for long-distance telecommunication. Corning had just exapted their skill in producing glass structures to create the standard of long-distance fiber optic communication. Digital innovation ecosystems have plenty of examples of exaptation. One major example is 3D printing. Three-dimensional printing is a digital innovation that itself started out as an exaptation of Computer Aided Design tools, advanced mechanical components, and advanced polymers and metal powders. As development and engineering on 3D printers has increased, their usefulness and capabilities have drastically increased. Modern 3D printers are involved in many exaptations within different industries. In manufacturing, 3D printers threaten to overhaul the systems currently in place and cause disruptions in how certain objects are manufactured.

Integrative Exaptations: A Modern Example
The Coronavirus Disease 2019 (COVID-19) pandemic has had interesting examples of both biological and technological exaptations, often the latter a result of the former. The virus resulting in the disease state COVID-19, SARS-CoV-2, was most likely initially present in bats. Whether the virus naturally mutated in bats or was genetically manipulated in a lab (and released accidentally) remains under debate, though evidence is mounting for the latter. Regardless of how the virus mutated, it become capable of infecting humans which is an excellent example of exaptation because the mutation allowed the virus itself to have a purpose when taken up by humans. The resulting realization by humankind of the threat COVID-19 possessed introduced a cascade of exaptations regarding crisis management. Many companies used existing machines and repurposed technologies to provide national and international demand of medical equipment and personal protective equipment. Many research laboratories used existing supplies and available personnel to begin research on COVID-19, SARS-CoV-2, and vaccine efforts. Exaptation was essential for these responses because time was the most valuable resource and building new systems, instead of exapting pre-existing systems, would have been too time expensive. When vaccines were developed and vaccination efforts began, logistic and distribution systems were exapted to provide efficient, time-sensitive delivery of vaccines. In Canada, the military was exapted to, in theory, provide efficient logistic flow of vaccines to distributors across the country. Vaccine distributors included health care locations such as clinics and pharmacies. But, vaccine distributors also included community centres and arenas which had been exapted to provide safe, efficient vaccine injections to the population.

Drift
Genes are passed on because of selection, as described above, but there is also drift. This is when genes or memes are passed on accidentally, not because they were selected for. To give an example, we will take Ghengis Khan, who a large portion of the Chinese population is descended from. Khan, like everybody else, had many mutations in his DNA, from copying errors and so on, that didn't affect his traits. But his descendents are very likely to have these same mutations. These random mutations that don't affect selection are nonetheless very common in the population because they piggy-backed on whatever adaptive genes Khan had. Through genetic drift a gene can become common even if it's not adaptive, and a gene can be extinguished even if it's not maladaptive.

The above methods of selection are pretty reasonable, in the sense that a trait is selected "for" a reason--a more efficient creature, for example. But sometimes traits can be selected without being selected "for." Suppose there is a small population of minks, and a few are darker than the rest. But the darker ones drown and are eaten for reasons that have nothing to do with their colouration. The dark trait would be eliminated from the gene pool, and the lighter traits would be selected, but not really selected for. They are selected due to chance. When large changes happen due to chance, we call it genetic drift.

Let's take another example of genes being selected without being selected for. Sometimes an organism no longer needs a phenotype--or worse, the phenotype it has is detrimental to a species' survival and reproduction. There will be selective pressure to remove that phenotype. In very small organisms, genetic material has a heavy cost. So a single-celled species, for example, will evolve to remove the genes completely. But in larger organisms, such as animals, carrying genes around is a negligible cost. It's "cheaper" for evolution to simply shut off those genes. That is, make it so those genes are simply not expressed, rather than erase them completely. What this means is that for large animals, such as humans, there are lots and lots of genes we carry around which are never expressed, and thus do not create a phenotype. Yet, the humans who carry them around reproduce. The result is that there are genes that are selected, but not selected for--because they have no phenotype that would affect selection, natural or otherwise.

Turning to memes, let's take, for example, John Grisham's 1991 the novel The Firm. The main character is named Mitch McDeere, but it is very likely that the success of this novel had nothing to do with Grisham's choice of this name. The novel would likely have been just as successful even if the character's name had been "Mitch McMaster," for example. But because the name Mitch was chosen, and it happened to be in a book that was wildly popular, the name "Mitch McDeere"was replicated millions of times. This can be seen as an example of memetic drift.

How Do We Know Evolution Is Happening?
Generally, there is so much evidence for evolution that some argue that it should no longer be even considered a theory, but a basic scientific fact.

Briefly, evolution is so widely accepted because it explains so much of what we observe in the world, far better than competing theories. Any alternative theory would need to provide plausible alternative explanations for these observations.

First, the fossil record shows that there were creatures who lived long ago that are no longer with us. The older the rock, the more different the fossils are from the species we see on Earth today. This strongly suggests that species change substantially over long periods of time. For example, the fossil record shows a transition from a horse-like creature long ago to modern whales. Unfortunately, fossils showing this smooth a transition is rare, because fossils are rarely formed and because we have yet to unearth many of them. But we never find fossils that look like modern mammals from geological areas that are 200 million years old. What kind of evidence could we possibly find that would cast doubt on the theory of evolution by natural selection in terms of how it is applied to life on Earth? Well, if we found a pre-cambrian rabbit fossil, it would be very disturbing. But this kind of counter evidence has never been found.

Second, evolution neatly explained the classification system already in place for the living world. Before Darwin, biologists had done extensive anatomical examination of hundreds of plants and animals and noted their similarities. Different species of cat, for example, had similar bone and muscle structure, so they were classified as being in the same group. At the same time, cats were more similar to other mammals than any of the mammals were to birds or lizards. The classifiers created a hierarchy of living things, but why this hierarchy should exist made no sense until evolution explained it: life evolved in a tree, with all living things evolving from a common ancestor. Creatures inherit the forms of the creatures that came before them, and rarely share forms with creatures from other parts of the tree. And evolution didn't just explain what we'd already found. Scientists looking at the similarity of creatures would speculate, thinking evolutionarily, on what their common ancestor probably looked like. When the fossils of those common ancestors were later found, they conformed surprisingly well with that the scientists speculated they must have looked like. This is not possible without thinking about evolution happening over long periods of time.

Third, genetic analysis allows use to discover the code of different species' DNA. The prevalence of this or that mutation allows us to construct an evolutionary tree of life. That is, genetic differences not only show differences between species, but specific hereditary pathways that occurred over the millennia. These analyses support (for the most part) the tree of life created by anatomists and explained by evolution.

Fourth, embryos often have traits of common ancestors that the adult individuals don't have when they develop. For example, bird and mammal embryos have gills that are later absorbed during development. No other theory can explain why this might be. According to evolution, all of these creatures evolved from common ancestors that had gills, and the genetic programming for making them never went away. Why it never went away was discovered later: they serve as markers for location in the developing embryo, so did not get weeded out by natural selection.

Fifth, many creatures have vestigial structures that are no longer functional, but still around. When a structure contributes to the survival and reproduction of a species, it is maintained and improved. But if a species changes its niche, and the structure is no longer adaptive, it gradually decays. But this takes a long time, so we have eyes on creatures who live their entire lives in the dark. The greater the nutritive cost of the structure, the faster it will be removed by natural selection, but in the meantime, vestiges of it remain.

The similarity of many animals is contrasted with how different animals look different if they are isolated from each other--by water, mountains, or great distances. Why do the animals (and all other living things, for that matter) look so different from those in Africa÷

Evolution in Life on Earth
Genetic information is stored in DNA. There are more or less identical copies of DNA in every cell of an individual organism. Processes in the cell use parts of DNA to create proteins, which do most of the work in biology. DNA is incredibly information-dense. It can hold the most information per unit volume than any other known medium, and is one quarter of the density allowed by the laws of physics.

DNA carries coded information. There is some ambiguity in how the term "gene" is used. We might think of the "material gene" and the "informational gene." A material gene is a particular stretch of DNA. If it replicates, it produces another gene. On the other hand, the "informational gene" is that sequence of nucleotides, everywhere it might appear in all beings throughout time. This is the sense of "gene" used when we say that you share some genes with your mother--she obviously doesn't share any of your material genes.

It is a twisted ladder-shaped molecule that can come apart and make copies of itself. The "gene" is a carrier of genetic information, and it is sometimes loosely defined. But one way to think of a gene is that it codes for a particular protein. Here's how it works: when a gene is "expressed," the DNA splits apart and another molecule, called "messenger RNA" makes its own copy of it. That RNA then uses that code to make a protein. The protein, then affects the body. Most of the action in a living creature is the result of protein interactions.

How, then, do we get the apparently continuous variation we see in living things? Siddhartha Mukherjee makes an analogy with pieces of colored cellophane. If you have seven of them, you can get just about any color by layering them on top of one another. The planes don't change, just the color you see looking through them. Similarly, you can generate nearly perfectly continuous external features with just three or five gene variants on any trait.

Variation happens because of changes in genes. Genes can change because for several reasons. At the level of the genome (the collection of genes in an organism), sexually reproducing creatures can mix genes with crossover. This is why children have genes from both biological parents. Single-celled organisms can often just give each other genes, a process called lateral gene transfer.

Genes can be directly changed by cosmic rays hitting them--this is the classic "mutation." Genes are copied, and very rarely there are copying errors, which introduce mutations.

tk epigenetics

Evolution as a Substrate-Neutral Process
“If you have variation, heredity, and selection, then you must get evolution”. –Dennett

Evolution is mostly broadly defined as a process of algorithmic optimization which occurs in systems where the following three conditions are met: Over long timescales, given relatively stable selectional pressures, there will be an incremental tendency towards forms which are best suited to those pressures. What is most significant about evolutionary thinking as compared to previous conceptualizations of the world is that it allows for non-directed development to account for what appear to be planned results. While this is typically thought of in biological terms, it is important to remember that as formulated above evolution is a substrate neutral process which can been seen to operate in wide variety of complex self-organizing systems. Probably the clearest example of non-biological evolution is found in the field of evolutionary computing whereby multiple solutions to a given problem are pseudo-randomly generated and then compete with eachother over multiple generations until an optimal solution is reached. This methodology has been productively applied to engineering problems where the problem space is vast, such as the design of antennas on space probes: the algorithm essentially serves as a guide through the design space by identifying potentially productive paths heuristically. Exactly how this applies to human cognition remains a contentious issue about which very little is fully understood. This chapter will sketch some of the ways evolutionary thinking may be applied to the questions asked by cognitive scientists. As such, our focus will be more methodological than “factual” per se. The final sections will briefly review the related fields of brain evolution, ethology/behavioural ecology, and evolutionary psychology and their contributions or potential contributions to the topic.
 * 1)  Existence and/or generation of variation
 * 2)  Transmission of variation (e.g. through reproduction)
 * 3)  Differential rates of transmission

Evolution on Multiple Levels
In terms of human behavior, evolutionary algorithms can be seen operating on several different levels and the process of teasing apart their interactions is a challenge because all tend to develop towards similar solutions to the problems faced by humans. While the processes by which they operate vary according to the substrate, ultimately the results are all judged against a similar metric, meaning that their outputs appear similar. The distinction of between levels in the broad sense we define it here is crucial to any informed discussion of evolution because the mechanism of inheritance varies with the substrate. The evolution of bacteria and that of higher animals, for example, can be distinguished in terms of the mechanisms available for the generation of new candidates: higher organisms (e.g. humans) reproduce sexually via the mixing of the genomes of one adult male and one adult female in roughly equal proportions organism whereas bacteria have the capacity for gene flow on a smaller scale between mature organisms. Mechanistic distinctions such as these can have significant impacts on the process of evolution and are something that will be touched on at several points in this chapter. Furthermore, none these levels exist in a vacuum; they all interact, sometimes in highly complex manners. For a good review of the broader philosophical implication of this perspective see Dennett (1995).

Biological
The study of biological evolution is the best understood of the levels at which evolution operates that are of interest to cognitive science. Artificial selection provides some familiar examples whereby biological evolution has resulted in significant alteration to the phenotype of a given wild species resulting in a distinct domesticated variant. Take for example the case of the domesticated dog (canus familiaris) of which there are hundreds of distinct breeds all descended from the wolf (canus lupus). Each breed has been selected on for many generations with human breeders with specific desired outputs in mind. In the case of artificial selection the fitness landscape is defined in the mind of the breeder and it is the degree to which an individual matches that landscapes that defines its reproductive success. In the wild a similar process occurs without the direction of a human breeder. The fitness landscape is defined rather by the likelihood of surviving to the age of reproduction (natural selection) and the in sexually reproducing species the odds of successfully mating (sexual selection). Darwin’s contribution to the field essentially boils down to the idea that given sufficient depth of time the selection mechanisms available in the wild would produce similar outputs to artificial selection. This has since been proven by extensive biological research, and is robustly supported by computational modelling.

Developmental
Some developmental processes, particularly with regards to the development of the nervous system, can be productively analyzed in evolutionary terms. This perspective was developed into a coherent theory in the 1980’s known as Neural Darwinism .	The genetic code underspecifies for the nervous system, instead using crossover events in development to generate a varied tissue type. (Sapolsky lecture ….. there must be a better source for this) Additionally, there are considerably more neuronal connections in the brain of a human infant than there are in an adult due to a process known as neural pruning. The development of an adult brain in the course of maturation is a process of evolution of this diverse, overpopulated, and overconnected neural population under environmental pressures. An interesting example can be drawn from the evolution of colour vision in primates. One might at first brush assume that this would involve changes to the genes coding for both the sense organ (in this case at the retina) and the parts of the nervous system responsible for interpreting the input from the retina. This is not the case, however (Katz 2011:2087)http://rstb.royalsocietypublishing.org/content/366/1574/2086.short. A change to the genes coding for the opsin molecules which attach to the retina in the presence of optic stimulus of a given wavelength is sufficient to increase the number of different colours an organism can perceive. In the presence of an increased variety of opsins the neural system will adapt to distinguish between this greater variety, much like a species will evolve to adapt to differing environmental pressures. This line of discussion now verges onto the highly technical field of the evolution of development (“evo-devo”) which is beyond our purposes here, but will be touched upon again in our discussion of brain evolution. A good review can be found in West-Eberhard (2003). Developmental plasticity and evolution. What’s most interesting about this from our perspective is the interaction of two evolutionary processes working across different timescales, both upon a population of organisms and on a population of cells within a single organism, conspire together to create a given output.

Cultural
Cultures can be considered in a similar manner to organisms or species, and doing so provides productive insights into the study of cognition. However, it is important to remember that unlike with biological evolution there is little to constrain the development or spread of cultural memes. Genes are identifiable and mutate and recombine in predictable manners. This is not the case with cultural elements because “memes” (the technical term) are more ephemeral and can spread and change from person to person and culture to culture in ways that no existing theoretical model is able to satisfactorily explain. A number of attempts to model cultural evolution have been made, with varying degrees of success, but it is important to remember throughout this discussion that the lack of an identifiable unit of transmission limits their predictive powers. The identification of memes is typically post hoc. It is sufficiently established that cultural elements can be selected for in nature, and certain Fijian food taboos for pregnant and lactating females provide the stock example of cultural evolution. Ciguatera poisoning represents a threat to this population as it accumulates in the predatory marine species which provide their primary source of protein (e.g. moray eels, turtles, sharks, several predatory fishes). While pregnant and lactating women can consume these species, doing so increases the risk of damage to the foetus or infant. The dietary taboos for these females correlate strongly with the relative risk of ciguatera poisoning posed by each individual species. This cultural feature has been demonstrated to reduce the chances of poisoning in pregnant females by roughly a third, and in lactating females by as much as two thirds. The stability, longevity, and widespread nature of this practice is predicted by its adaptive benefit, and borne out by historical sources on the region. The overall outcome is such that the rates of ciguatera poisoning in pregnant and lactating females are significantly less than for the population as a whole. The fact that these females report craving these taboo food sources, and having to consciously resist these cravings, suggests a cultural rather than biological mechanism of inheritance.

Mechanisms of Cultural Evolution
Where in biological evolution the information is encoded in genes, which are inherited genetically, in cultural evolution ideas are represented as memes, which are reproduced perceptually.

Note that the structure of cultural evolution differs from that of the biological evolution of higher organisms in four keys ways:

The Baldwin effect is worth touching on briefly at this point because of the way it relates cultural and biological evolution: in its original conception it can be broadly defined as “a sequential process in which acquired characters (e.g. culturally evolved characteristics) are replaced by genetic characters (i.e. biologically evolved characteristics).” This is useful starting point, but remembering the discussion above about interacting levels of evolution we can see how it sets up a false dichotomy. In its more current specific usage the term refers to how learned behaviours can become reflected, and partially determined, by the genetic code (ie. “instinctual”). Birdsong, for example, is more or less wholly learned in some species, more or less wholly genetically determined in others, and every shade of grey in between for still others. While it is not experimentally proven that this is distribution is caused by the Baldwin effect, the data does lend itself to such an interpretation. Computational simulation suggests the Baldwin Effect is real.
 * 1) Horizontal transmission – as with lateral gene transfer in bacteria and archaea, memes can be passed between adults lacking a close family relationship rather than being limited to parent to offspring transmission
 * 2) “Generation” lengths are variable – the lifespan of a given meme is difficult to define, some cultural elements persist relatively unchanged for vast spans of time, whereas others are passing fads (e.g. pet rocks, popular music)
 * 3) Direct copying of phenotype (rather than genotype) – i.e. it is the cultural behaviour, attitude, etc. that is transmitted rather than the underlying neural or biological mechanism
 * 4) Enculturation is a gradual and ongoing process throughout the individual’s lifespan which creates a coherent system – the history of enculturation will therefore partially determine the memes that are amenable to acquisition

Culture Beyond Evolution
Philosopher Daniel Dennett describes early cultural evolution as "profoundly Darwinian," but over time, as we developed language and other ways to think, the changes became more like intelligent design--human planned cultural changes.

Evolution of Homo Sapiens: Communication and Collaboration
It is common knowledge that the human species has gone through a significant evolution over the last 5 to 7 million years, but few people know how or why this occurred. The first modern humans, also known as homo sapiens, first appeared on this planet 200 thousand years ago and quickly became one of the most powerful species on the planet. A transformation like this does not just happen by mere coincidence. It is a result of natural selection and adaptation to the environment. Humans did not always “rule the world” like they do today, however, the capacity to adapt and most importantly to collaborate has turned the human species into what it is today.

Before humans could simply go to the store and buy themselves food, they had to hunt to survive. This was not always easy because, compared to most other animals, humans are quite slow. To be able to hunt effectively humans learned to travel on two feet instead of all fours because they realized that since they were not fast enough to catch prey, they needed stamina. Traveling on two feet instead of all fours requires significantly less energy, so humans would chase their prey at a slower pace for longer until their prey tired themselves out. Not only that, but with their two extra limbs, humans were now able to carry weapons as they previously could not overpower their prey. This is a clear example of evolution brought on by natural selection.

Another key to human success as a species is the ability to communicate and collaborate. Collaboration as a species allows humans to accomplish goals that are otherwise unattainable by an individual. While many other species can collaborate as well, none do it as efficiently or in other words as well as humans do. This is due to the fact humans can speak, a trait that humans did not always have. This ability is perhaps one of the most important steps in human evolution.

It has been theorized that humans learned to speak for many different reasons. One of the most interesting of them is that humans learned to speak to help to make tools. An experiment led by Thomas Morgan, a psychologist at the University of California, tested this theory by having five groups work on making Oldowan tools. Oldowan tools are stone tools first used around 2.6 million years ago that can be used to create different types of tools whether it be for weaponry, butchering, or really anything humans would need. Each group had the same objective, but each with different rules. The first group was given a core, a hammer, and examples of some finished products, and were not allowed to communicate at all with only the examples as guide. The second group learned to make tools simply by observing the first group, again no communication was allowed. The third group were allowed to show each other what they were doing without gesturing and without speaking. In the fourth group, gesturing was permitted, but still, no talking. In the fifth and final group, a group member was assigned as the “teacher”. The teacher was permitted to talk to his groupmate to help make tools. Results of this experiment showed that the first three groups struggled and had very little success. In the fourth group, where gesturing was permitted, the tools were twice as effective as the first three, however, in the fifth group in which speaking was permitted, results showed that the group performed outstandingly compared to all four other groups, as the effectiveness of their tools more than doubled those of the fourth group. It was concluded that to make viable tools for survival, there had to be some capacity for teaching, and possibly the ability to speak.

Homo Sapiens' incredible ability to speak was not wasted. Early humans used this to help each other find food and share it with each other, this marked the beginning of modern society. Small communities worked together to create small villages in which people would help each other to build shelter in order to not only survive but live a comfortable life. Over time, small villages turned into larger villages which turned into small cities which eventually turned into the large cities of today. The comradery experienced by those who lived in the same villages or cities led to modern civilization.

Using their unique ability to speak and collaborate effectively, humans were able to learn from previous generations which helped them to grow increasingly powerful as time went by. As mentioned, humans were able to develop more sophisticated tools through collaboration. The ability to speak to each other allows humans to understand each other and share their desires with others, which is ultimately what led to the creation of civilization and society.