So I've decided to help enlighten those who don't understand evolution and thus I've taken it upon myself to put together a summary of the knowledge necessary to truly understand the concept. I would highly appreciate questions as well as any holes in my explanation pointed out. The purpose of this post is to serve as a final word against creationism.
edit: Improved readability and fixed many minor grammarical errors.
edit2: Added links to questions within thread for those interested in reading other information related to evolution.
Chapter 1: Background knowledge
What is a theory?
Understanding evolution in its entirety is no easy task. Many scientists can spend their entire lives studying the concept and still hesitate to tell you they understand it entirely. Evolution is a theory that we’re constantly improving and adding to. In order to understand what a theory is it’s important to know what science defines the concept as.
In scientific terms there’s roughly four different statuses and idea can have; Idea, Hypothesis, Law and Theory. An idea is a pretty general term for just about any thought or concept. Ideas vary all over the place and may sometimes become synonymous with higher levels of credibility however it’s important to note that not all ideas are created the same. All theories are ideas but not all ideas are theories.
A hypothesis is a proposed idea about something which has not yet been tested, Hypotheses are generally educated guesses at why something acts the way it does. Hypothesis are typically reducible to different concepts and usually represent a bridging between two concepts. In this way whether the hypothesis is wrong or right something is told about the relationship when tested.
A law is a mathematically reducible concept that applies (as far as we know) universally. Laws describe how something acts typically in a mathematical fashion. Generally speaking were a law to have variance in the universe the universe as we know it wouldn't be possible and as such, unless we find otherwise (and in turn account for said variance) laws are considered universal. This is a common principle of science called the principle of universality. Unless otherwise noted we assume that all parts of the universe act the same. Laws can be wrong; however this rarely necessitates the abandonment of the law. For example newton’s laws on gravitational attraction are still utilized today in basic science classes. While relativistic models describe how gravity acts much better they typically are complex in the way that prevents their easy dissemination to those unfamiliar with the concepts in the first place. Hence we tend to teach the simplified version which may be technically wrong first before teaching the much more complicated version which as far as we know is correct.
A theory is not necessarily mathematically reducible. A theory attempts to describe why, and what happens within a given system. The theory of gravity describes why gravity occurs, not necessarily how it acts. The germ theory describes why disease occurs not necessarily how diseases will act. Etc. A theory must be accepted by the scientific community at large to be considered valid; although some controversies between theories are possible the controversies are usually over two competing theories’ explanation of one law. Theories are generally highly tested and their explanations are considered factual. If a theory is in error it’s usually a small portion necessitating a small alteration. Theories cannot be disproven only shown to be incomplete. A discovery of an animal created by 'god' tomorrow does not erase the mountains of data we've found that demonstrate that most animals have indeed evolved, it only subtly alters it.
A theory typically has a pattern component and process component to it; a pattern that is observed and the process that is occurring or the explanation of what is occurring. In understanding these definitions it’s important to note that a theory is not simply an idea and that it’s a factual claim of the world surrounding us. Thus the theory of evolution describes what and why animals diversify, it is not likely or even possible to ever be 'disproven' although it may adapt to new knowledge (such as DNA) which explain inconsistencies within the theory.
Brief history of evolutionary thought:
Evolution has been a philosophical idea for more than two thousand years. Our first evidence of evolutionary concepts explaining life come from religions dating to 5000 BCE. However these concepts shared several characteristics. The common conception of evolution of life was that humans represented the pinnacle of evolution with life progressively evolving from that point upwards. This concept was often referred to as the ladder of life with the ultimate purpose of life being to produce something greater than before. Evolution is not progressive or hierarchical. Furthermore evolution creates pathways that are in most cases one way. Animals rarely become more simplified and often in the process of becoming more specialized they close off evolutionary pathways. That is to say, our nose will probably never evolve into an elephants trunk, it may however disappear all together.
The secondary concept to this was the idea of spontaneous generation. It was assumed for much of human history that life, especially small life arose from the inanimate objects around us. For example, if we left rotting meat out it would eventually transform into magots which would transform into flies etc. The concept was wide-spread and it wasn’t understood until recently that life originates from other life. Thanks to this concept pasteurization was made possible. No matter how many human generations you allow your wine to sit in your cellar it will not turn into flies and it will probably never go bad unless it's somehow exposed to the outside environment. Moreso the concept that purer and purer materials result in the creation of higher and higher beings is obviously flawed.
Another concept of the time was essentialism, the idea that species had small divisible 'bits' which were in essence their species which in turn drove their future evolution. Many of the animalistic characteristics (half animals, half humans etc) of mythology of the time was driven by this thought. A person who’s heritage was a fly would still possess those essential characteristics. Similarly while rotting meat had the essential characteristics of flies, a flower might have the essential characteristics of a butterfly. Most of these concepts as we know them originate in Aristotlean thought. While they represent a step forward they also represent a step back.
Anaximander of Miletus was one of the first we know to propose that animals could turn into other animals. In his idea even humans were descended from other animals. He believed that humans and all land mammals had descended from a fish like creature that had lived in the oceans eons past. Truly in hindsight his conceptions were probably superior to the ones Aristotle proposed which were considered more valid. Alas popularity is not a good measure for reliability.
Empedocles was perhaps the first to target the birth and death of animals as the quintessential factor in allowing evolution to take place. He believed that the environment was composed of different elements (appealing to the elementist ideas of the time) composed in different complexities that were additive or destructive. Some elements, through random happenstance would occur together to allow the survival of a creature, he considered the vast majority of these combinations to be ‘unsuccessful’ and producing inanimate life. As animals died they released these parts back to nature which could again be recombined to form other things. Once the elements did produce an animate animal however the animal would persist so long as it could reproduce almost as a template for future combinations of elements. Another step in the right direction to be sure however it also implies that animals can arise independently of each other.
Then came Plato. Plato dealt perhaps the most damaging blow to biology which buried his predecessor’s ideas. With the idea of essentialism taken to the extreme he believed animals all had a perfect form from which they varied due to imperfection. These perfect forms or essences had been written into reality by an all-powerful creator and thus, the ‘perfect’ universe was one with life. This theory became the dominating ideal of the time and for the next two-thousand years. One might note the similarity of this to creationism perpetuated by the Christian church. This wasn't an end all to discussion on the subject but, Plato had set the ground work for the future Christian schools of thought. Many people did still believe that these essences could be altered or even evolve into other essences.
Aristotle was Plato’s student and he remains as one of the first scholars or historians we have real direct knowledge about. Aristotle retreated to the island of Lesbos to study life. With the influence of his teacher under his belt he produced four definitive works on his studies of life. De anima (on the essence of life), Historia animalium (inquiries about animals), De generatione animalium (reproduction), these works became the standard thought of many scholars for millennia to come. His works produced some wonderful interpretations that border between the genius and the mythic. With many observations that did indeed reflect reality Aristotle’s greatest contribution was the ladder of life.
Also known as the scala naturę, although not a proposed mechanism of diversity it served as a hierarchical description of life similar to today’s taxonomic ideas in some respects, however taxonomy is not hierarchial. Placing his animals in a list from those he considered most life like to those he considered least produced a transition from those organisms which were least lively (less likely to move) to those that were most (us). In reviewing his scala naturę Aristotle came to the conclusion that the creator of life essences had had a final ‘cause’ in mind in creating the different species and that thus, life had purpose. From that point on it became standard to view life as having a purpose. This view became known as teleology.
The opposite side of the world had no such difficulties however. Taoist philosophy held that everything in the world or universe was in a constant state of change or flux. Thus life had adapted to its environment. This view which is identical in many respects to modern evolution was held as early as the 4th century BCE. Chuang Tzu was one such Taoist philosopher who we know of to author the direct relationships on the adaptability of life. Chuang Tzu explicitly denied that species of any sort were fixed or imbued with essence.
Still rational thought in the west was not yet suppressed by orthodoxy. Roman philosopher, Titus Lucretius Carus the famous atomist wrote the poem On the Nature of Things. Amazingly the poem describes the origins of the universe, earth and life from a completely naturalistic standpoint. Unfortunate his ideas of evolution were largely ignored until the Poem’s rediscovery in the Renaissance.
After that the Christian story of Genesis quickly became the most well known explanation on the origin of life and everything until the 4th century this remained largely unchallenged. Augstine of Hippo was one of the most surprising contributors to evolution. While he considered the nature of Humans and Angels to be perfect, Augstine thought that, “plant, fowl and animal life are not perfect ... but created in a state of potentiality.”; which was further defined as life transforming over time; perhaps over many hundreds or thousands of years. Augstine of course pushed for a less than literal translation of the genesis story, stating that the story is more important to understand the relationship of god with man than the relationship of life’s origin and diversity. Thanks to him the catholic church was eventually able to decide the the theory of evolution did not conflict with their theology at all, though it took many thousands of years to do.
Islam was the next contributor to the idea of evolution. Scholar Al-Jahiz wrote in his book The Book of Animals that, “Animals engage in a struggle for existence; for resources, to avoid being eaten and to breed. Environmental factors influence organisms to develop new characteristics to ensure survival, thus transforming into new species. Animals that survive to breed can pass on their successful characteristics to offspring.” The book became a majorly formative work in the Islamic world and was rediscovered by the west during the enlightenment. Most importantly the book was known and read by Darwin’s predecessors who contributed to the final form that was presented in the book, On the Origin of Species.
Perhaps more important was this paragraph: “We explained there that the whole of existence in (all) its simple and composite worlds is arranged in a natural order of ascent and descent, so that everything constitutes an uninterrupted continuum. The essences at the end of each particular stage of the worlds are by nature prepared to be transformed into the essence adjacent to them, either above or below them. This is the case with the simple material elements; it is the case with palms and vines, (which constitute) the last stage of plants, in their relation to snails and shellfish, (which constitute) the (lowest) stage of animals. It is also the case with monkeys, creatures combining in themselves cleverness and perception, in their relation to man, the being who has the ability to think and to reflect. The preparedness (for transformation) that exists on either side, at each stage of the worlds, is meant when (we speak about) their connection.”
While certainly not perfect as animals don't transform into other types of animals, you'll never see an elephant become a snake and such thing is impossible, it was still a huge leap forward considering humans to be descended from monkeys. Although how snake-like an elephant could become is debatable. Regardless animals differentiate into their descendents they do not go backwards (in most cases) and then come out again as a different animal.
Christian thought remained to lag behind the Islamic thought, and in the 12th century as Islamic and Greek works were introduced into the christian world Thomas Aquinas utilized them to create a new scala naturae or great chain of being combining ideas of essences with the grace and majesty of god.
Finally a real biologist arrived on the scene, Jean Baptiste Lamarck loved to study life. Lamarack was a brilliant scientist and philosopher of the time and introduced the concept of transmutation of species in his book Philosophie Zoologique. This differed in key ways from the modern theory of evolution, however it represented the closest approximation to modern theory yet. Lamarack didn’t believe that all species shared a common ancestor (a concept later proven wrong by Pasteur) but rather evolved continuously higher and higher starting with independent spontaneous generation. After genesis the life forms would then adapt and spread into new environments which would then force the creatures to evolve new adaptations somehow.
Unfortunately the scientists of the time had no clue how or why adaptation occurred. Though heredity had already been explored by Mendell, his works had been largely ignored until the 20th century when they were ‘rediscovered’. With the mounting evidence that the theories of transmutation did not answer the question entirely many scientists pressed that the reason was because the species had been designed in perfection by a creator. A few scientists held on to the idea however that the best explanation for the diversity of species, especially similar species in different but similar locations was transmutation.
The Renaissance: Darwin and Wallace
The players were in place and the stage had been set. With the waning of the power of the church and the ability of printing presses to distribute ideas across the world, the old world knowledge soon became known to the curious few who choose to study such things. One of those people was known to Darwin.
Darwin was something of a gentleman. Independently wealthy he had no real interest or need to work. His father however saw the calling as something of a character building exercise. Become a doctor or join the clergy were the two options Darwin was given. Not particularly fond of the church already Darwin chose to become a doctor. Alas he tended to faint at the sight of blood which given the rather barbaric methods of teaching and the lack of anesthetic at the time was more than understandable.
However Darwin was anything but stupid. He did well as far as theory was concerned and his mind seemed up to the task of understanding complex ideas and science; with no career as a doctor Darwin was facing the uncomfortable future as a member of the clergy. Unbeknownst to him his professor had submitted his name to study abroad on the HMS Beagle. The ship was destined to sail around the entire world charting the coastlines, the fauna, local animals and everything in between. The voyage was to take one year. Seeing it as a good opportunity to delay the inevitable or even to find a different calling Darwin jumped at the chance.
Although the HMS Beagle was a bit off schedule, by about four years, Darwin was able to have a lot of fun. His primary duty was to sketch the shoreline however he took extensive notes. As naturalists were accustomed to at the time he also caught and stuffed every animal he could get his hands on, not to mention eating most of them too. One particularly rare specimen he recovered was rescued from the trash after dinner, despite weeks hunting for the bird the cook had accidentally caught the specimen in a net for dinner.
Merely months after setting out the HMS Beagle began to swell with specimens notes and information. So productive was the trip that soon the Beagle had to ship specimens home to avoid being overloaded. Thousands upon thousands of specimens and pages of notes made their way back to England waiting for Darwin to one day decide to derive some sort of meaning from them.
Darwin was also noticing patterns in the species he collected. He marked many of his ideas down in his notes. It seemed odd to him that there was a squirrel like creature for example in Africa that was nonetheless not a squirrel a dog like creature in Australia that was not a dog and etc. Around the world this oddity repeated itself; animals which fit the same place as more familiar animals from his home but nonetheless were unrelated. He wondered why a creator would bother creating different animals for the same task and questioned whether life was designed as perfectly has he had been taught. Darwin was aware of the heretical ideas at the time and the more he looked at the specimens he caught the more he wondered if the scala naturae was flawed.
Still the theories were vague in their inception and it did not seem that Darwin truly paid much attention to the ‘science’ part of his scientific expedition preferring instead the adventure, killing exotic animals and eating them. For uptight gentlemen with strong Victorian sentiments the liberation probably seemed intoxicating to him.
It was not until the Beagle arrived in South America that Darwin penned his first rough ideas of evolution. Called the tree of life, it was the product of Darwin’s daydreaming of the Galapagos finches. The Galapagos makes up a large chain of semi volcanic islands off the tip of south America in the pacific ocean. Extremely diverse with life each island is far enough away from each other to severely restrict the movement of animals.
Of particular interest were the finches. The Galapagos contained (back then) about fifteen distinct species of finches. They were all definitely related to the common finch that had one morphology in England however they each possessed unique adaptations. Morphologically this qualified them as different species (although DNA-wise there’s fewer truly distinct specimens) and the question remained, why?
Darwin’s idea started with a hypothetical common finch flying from the mainland of South America. This finch landed on the first island. Darwin noted that each of the islands had different plants, and different types of resources. This first finch undoubtedly found a way to find some food and survive and moved on to the other islands slowly over time. Finches have major difficulty flying between the islands themselves, but on one stormy night he happened to observe birds blown far from their homes and even some from neighboring islands. This was a eureka moment.
If the birds were introduced into new environments where each could survive poorly but not as well as in the varied environment of the main continent then the birds would become competitive with one another. This competition would drive the weaker less effective finches to essentially lose out on the limited resources; this in turn would bias the heredity of their descendants. Darwin had already seen human inspired examples of this with selective dog breeding. If only the finches with the bigger beaks are allowed to reproduce then naturally the population will achieve bigger beaks over several generations.
This formative conclusion had vast implications when applied over a much longer term. Combined with the knowledge that the earth was millions of years old or older (Estimates were based on rates of erosion, which was obviously flawed) Darwin had all the pieces of the puzzle staring at him in the face.
Still Darwin was a bit of a procrastinator. His friend Alfred Wallace was coming to independent conclusions of evolution in his own way. Alfred was a bit jealous of the journey Darwin had taken on the HMS Beagle, thus he became his own naturalist on the ship HMS Mischief. The ship took him to the Brazilian rainforest to study the plenitudes of species and hopefully sell odd specimens to various collectors throughout Europe. Wallace and Darwin had both exchanged ideas on the transmutation of species and Wallace’s primary goal was to find evidence of said mechanism.
After losing his younger brother to Yellow Fever and five years in the amazon, Wallace was ready to return. On his journey home however the HMS mischief caught fire taking his specimens with it and nearly Wallace as well. A smaller vessel luckily was able to rescue the crew and despite low provisions the ship was able to make it back to the UK. Wallace languished for some time in the UK writing several books on his journeys to the amazon, only able to save his diary from the journey and the few specimens he had sent back to England.
Darwin by this time had begun looking into his specimens and had penned less rough idea of his conception, his tree of life was slowly taking shape. However after being home for more than decade one might expect a bit more from the relatively lucky Darwin. Wallace was not so lucky but would not give up, exchanging ideas with Darwin only validated his theory moreso. Wallace chartered another expedition from to the west indies, This expedition proved much more fruitful and after collecting hundreds of thousands of specimens Wallace’s luck was changing and while in the West Indies Wallace had a similar eureka moment to Darwin noticing the adaptations from island to island.
Home again Wallace began to pen his theory of Natural Selection. Hoping to impress his friend Darwin, and trusting him to review the work Wallace sent his manuscript to his friend. Darwin had scarcely done much of anything with his work by this time and other than a tree of life drawn on the scientific equivalent of a napkin Wallace was far ahead of him. Darwin was utterly shocked. Wallace had come to the same conclusion he had and worse, his manuscript was ready to go. With only a year till presentation at the Royal Society Darwin quickly honed his ideas into a more thorough manner.
Together, Darwin and Wallace presented their theories at the Royal Society shaking the established ideas to their cores. Though the transmutation of species was already known of, the theory was considered radical at the time and was unsupported by most naturalists. Darwin’s journey had convinced him that transmutation had occurred, while Wallace had journeyed already believing in the concept. The two perspectives meshed beautifully establishing both the formative knowledge needed to come to the conclusion and explaining the relationships involved.
What is surprising is just how good their theories were. They described embryology, homology of structures, the fossil record and geological timescale of existence, pasteurization and the concept that life only arose from other life, they described the principles of breeding with animals and livestock and finally asserted the ultimate selector of the natural world. Death.
One small problem still remained: there still existed no known mechanism for heredity. Darwin’s explanation relied upon his theory of Pangensis, to which he supplied as his explanation of breeding techniques in domesticated animals. Under his theory small perhaps atomic scale bits grannules called gemmules contained certain information about heredity and the environment itself. These gemmules would concentrate in the reproductive organs providing the progeny of the next generation information on what adaptations to make. Other scientists were quick to point out that though some animals like dogs were readily altered by the guiding hand of breeders many animals were quite resistant to such changes. Furthermore most observations of new features in animals were mutations that resulted in an imperfect specimens, without understanding heredity and the fact that mutations don't necessarily mean the difference between a third arm and two. darwin unfortunately was unable to contend with these issues.
Chapter 2: A brief description of Biochemistry and Heredity
So then what is Heredity? Well Heredity simply put is the traits passed from a parent to their offspring. The first real research on the subject took place hundreds of years ago in an isolated monetary. Gregor Mendel was a monk who had designed a series of controlled experiments comparing the traits of peas and flowers and the traits of their offspring. What he discovered would have shook the core of understanding of life had it not taken till the 20th century to discover it.
What Mendel had stumbled upon was the process of genetic recombination that was responsible for heredity; chromosomes, genes and alleles. Although he could not know for example that the chromosomes were composed of DNA wrapped tightly around histone proteins simply by observing the proportion of offspring following differing generations, the information he did derive was groundbreaking. Genetics are mathematically reducible and occur in an expected way.
We are what is called Diploid organisms, This means that we have two alleles or genes at every locus (position) within our chromosomes. Gregor happened to be lucky; the traits he had chosen happened to be located upon different chromosomes and happened to resemble the inheritance we’re familiar with. Plants actually have a much more complicated system of genetic recombination than our own and may have far more alleles than just two or as little as one. I digress though and plant evolution is another topic entirely.
We receive half of our chromosomes from our father and half from our mother. As our reproductive organs produce reproductive cells (eggs and sperm in humans) they split into haploid cells. These cells only have one allele for each gene. These haploid cells then undergo a series of recombination events that allows them to randomly distribute which half of their chromosomes (fathers or mothers) goes to which cells.
To put it another way, I have black hair which is a dominant trait. Let’s call this gene the B gene. My mother has blonde hair which is a recessive trait, let’s call this the b gene. Thus I received on B from my father and one b from my mother. The combination of these two genes creates what I genetically receive as hair color. Because the black hair of my father is dominant I have black hair. However my sperm may carry either the B or black hair allele or the b blonde hair allele. This in turn means that my children can either have black hair or blonde hair depending on who I mate with.
This allows different traits to be paired up in unique ways and also helps ensure we’re not all related to each other. This relationship was exactly what mendel had described. He had found that peas with the yellow color were dominant over peas with the green color and he wrote this relationship as Y for yellow and y for green. By crossing pure green peas with pure yellow peas he produced a generation of entirely yellow peas. This relationship can be visualized with the help of a Punnett Square. Punnett squares are very simple graphical representations of possible recombination of genes. Humans have as many as 20,000 genes which in turn code for some 100,000 proteins which in turn make everything we are composed of. A punnet square that size is a bit more complicated so we use the mathematical relations inherent in this diagram to derive the possible options each individual might have.
As you can see the mixture of a pure dominant and pure recessive creates a generation of mixed offspring all which physically manifest the dominant allele. Mendel then crossed the second generation with itself this process is called self-fertilization and many plants are more than happy to do so. What this allowed him to do was to observe what would happen amongst the mix offspring. If we look at our punnett square and transpose the new genes into the diagram we can see that the relationship is fairly simple.
As you can see 75% of the third generation has a yellow manifestation of their genes. This is called the phenotype. However genetically only 25% have two yellow alleles paired, half have one green allele and one yellow allele and the last quarter has two green displaying the green as its phenotype. The difference between one’s phenotype and their genotype can be quite dramatic when you think about dominance.
Mendell went further than that though; he noticed some traits were tied together, as though located on the same chromosome. Using the same punnett squares we can describe what he explored in slightly more detail however this is quickly approaching the limit of the effectiveness of punnett squares, for more complicated heredity we rely upon mathematical expressions.
Finally Mendell also discovered that some traits were additive, some traits shared dominance, and other effects within the heritability. The totality of this was a seemingly random new generation that actually has a mathematically predictable ratio of phenotypes and genotypes.This is the missing hole in Darwin’s theory. If we for example, dislike our peas to be yellow because it’s unappetizing (modern food industry) we might choose to kill off the yellow peas producing future generations which are biased towards the green allele being present in a higher proportion than in the generation preceding it.
What is it called when the Allele frequency within a population changes due to selection? It is called evolution. This is in a nutshell what evolution is. Now this foundational knowledge does get a bit more complicated if you delve into it further, sometimes many genes act in concert together, sometimes a double copy of a gene is required, sometimes genes are made silent. Furthermore during sex genes have the opportunity to duplicate themselves, to swap places, to become related to other structures, or to become silent. Sometimes these genes still work partially but their products are ineffective or inefficient. Sometimes their products are better.
So changing the allele frequency in a population is fine and dandy and can easily explain why the finches of the Galapagos varied from one another, and why our children look the way they do. This certainly can lead to for example a bigger human, a smaller human, a more intelligent human or a less intelligent human. But these are ultimately still humans are they not?
The answer is a hesitant yes. Changing the allele frequencies in a population does not lead to new species in most cases. That’s not to say it can’t it certainly can especially if two species have different selection pressures. This is why the Galapagos was particularly important. On some islands hard seeds were the primary food sources; on others nectar and flowers were more common. This produced finches uniquely suited to their food sources and because the original finch populations arrived so many thousands of years ago each island has been evolving independently with different types of selection. For example hard nuts require big beaks, whereas nectar requires a beak more reminiscent of a humming bird.
The two big factors in introducing new genetic information are mutations. Mutations happen both in the first stage of manipulation of our genome into our sperm or eggs, sometimes genes aren't split perfectly in half as they should be, sometimes they switch places, sometimes they're duplicated more than they should be. Once again when animals produce offspring sexually do these genes have opportunities to recombine, duplicate, transpose or otherwise change. This is where much 'new' evolution comes from.
Chemical Evolution and Abiogenesis
The concept of chemical evolution is one that is highly contested by modern Christian apologetics, for what reason is anyone’s guess. The likely answer is that chemical evolution is slightly more complicated than basic evolutionary theory and as such is an easy target to use misinformation to defeat. Chemical Evolution is fact. Simply put it’s the product of the laws of chemistry in action; which is to say, chemistry alone contains the basic concepts which would lead to the creation of life.
That’s definitely a bold statement but it is one that every chemist accepts and knows. The pattern component of this theory is very simple. Early earth contained a variety of chemicals and compounds that recombined at random to produce increasingly complex structures. How could this occur?
Well first off there’s the beauty of carbon. Carbon is a particularly excellent element. Extraordinarily common, Carbon can also bond with numerous other atoms to form complex molecules with carbon acting as a backbone or framework. The other important ingredient was water. Water is an excellent solvent and can dissolve most things due to its polar nature. Because of this Ionic compounds disassociate within water. Hence life is made primarily of contently bonded compounds which utilize ionic compounds dissolved in water.
Now many carbon molecules can be made simply by virtue of being carbon. Unfortunately many other reactions require input energy in order to generate complexities. What gave us this energy? Well several things contributed to it. Lightning bolts today can create all of the life creating compounds needed to start prebiotic life. Volcanic eruptions release vast quantities of complex compounds necessary to start prebiotic life. Finally meteors bathed in the radiation of space release vast quantities of complex compounds upon impacting planets. All of these contribute to the formation of three primary types of organic chemicals.
Amino acids are rather simple chemicals to form. They consist of a simple amino group (NH2) and a simple carboxylic acid (COOH) group bonded to a central carbon. Off of this carbon is an R group which specifies the type of amino acids. These are rather simple structures but they in turn make up just about everything structurally about who you are.
Now simple amino acids alone aren’t proteins, it requires chains of amino acids to form proteins. How does this occur? Well simply the carboxylic acid reacts with the amino group. One hydrogen is lost from the amino group and the OH is lost from the carboxylic acid to form H2O or water. Because the amino group and carboxylic acid become unstable in this configuration they covalently bond to restore balance. This step is repeated dozens, hundreds, thousands even millions of times to produce proteins composed of 20 distinct types of amino acids. These proteins make up almost every type of structure in your body from the color of your eyes to your blood type. These 20 amino acids are shared by every life form on the planet.
The next thing needed for life is lipids or fatty acids. Fatty acids are composed of of a simple carboxylic acid attached to a chain of carbons and hydrogens. These in turn have a variety of distinct properties. Most notably they are non-polar meaning that fatty acids do not dissolve well in water. Fatty acids also have the ability to bond with other molecules in a similar fashion to the peptide bonds off of the carboxylic acid. This allows them a particularly interesting ability. If they bond with a polar molecule (one which has a net charge) they can become amphipathic. This means that part of their chemical structure hates water, and part of it loves water.
Why is this significant? Well, have you ever wondered what your cellular walls are composed of? Besides a significant number of protiens and carbohydrates the cellular membranes are primarily composed of layers of fatty acids. These fatty acids organize themselves so that they form a membrane spontaneously. The reason they do this is simply because the fatty acid head loves water while the tail is nonpolar and dislikes it. This attraction within liquid forces the fatty acids into a spherical shape on either side a fatty acid presents its head to the water with a layer of fatty acid tails in between.
These first fatty acids were critical to the formation of life because they allowed something that was truly life like to occur. Chemistry within a localized spot that was different than the chemistry occurring in the outside environment; which is to say, a fatty acid bubble can have unique chemistry to the outside world occurring within it. This is the basis of our cellular membranes. It’s key to remember that fatty acids arise entirely naturally and that examples are known that contain various other important chemicals. In fact this is how your laundry detergent works and why soap commonly uses animal fat.
Then we have carbohydrates. Carbohydrates are simply a word for a carbon paired with a water molecule. The simplest carbohydrate is CH2O with far more complicated carbohydrates composed of repeating units. Carbohydrates are most known for their utilization for energy in all sorts of life forms. Essentially carbohydrate producing lifeforms form the basis of life on which almost all other lifeforms depend. However before carbohydrates existed and the capacity to fix carbon existed organisms relied mostly upon nucleic acids and chemical energy. For example some of the earliest known organisms lived by oxidizing iron within water. This process was pretty inefficient and it’s mostly utilized by organisms which have no predatory capacities or ability to reach sunlight.
Lastly we need nucleic acids. Nucleic acids are unique in that they provide both energy and a blueprint for future development. Nucleic acids are composed primarily (in biology) of five different chemicals. Uracil, Adenine, Guanine, Cytosine and Thymine make up the very basic form of two important structures, RNA and DNA. These in turn are composed of a nitrogenous base, a phosphate backbone and a pentose (five carbon) sugar.
What is DNA? Well most people understand DNA, dna is a very stable way to transmit information. While mistakes are made they’re very infrequent and many inbuilt mechanisms are present to detect mistakes if they do get made. However DNA deliberately has inbuilt mutational mechanisms.
What is RNA? RNA is a very unique and exciting chemical. Essentially it’s composed of one side of the double helix in DNA except thymine is swapped out for uracil (which is slightly more stable). RNA however has another unique function. RNA can act as an enzyme and will synthesize proteins on its own. This is quite exciting because it means that with carbohydrates, lipids, and amino acids every ingredient necessary for life exists naturally.
Now it requires understanding a bit of mathematical probability. The probability of chemicals coming together to produce a life form is rather low. However so long as there is time life has the chance to reroll indefinitely.
At some point about 3.9 billion years ago after some 500 million years of rolling the dice the ingredients came together, and life was formed. Because of the difficulties involved with this process life probably only evolved once and any other life that may have formed by happenstance was unable to compete with the earlier form.
Most evolution takes place in response to novel food sources, novel environmental conditions, and sexual competition. Still this doesn’t alter the base body plan much. So how did humans evolve from cells? Before we answer that question let’s go back to the beginning and explore the concept of a species.
Chapter 3: What is a species?
Now before we get into the actual process of evolution of life it’s important for us to know what a species actually is. There’s not a singular definition for this in science mainly because the lines which differentiate one species from another are difficult to understand. Phylogeny is the study of a species via it’s DNA and produces the most accurate representations of species however sequencing DNA is a long and expensive process currently and though many thousands of species have been sequenced since the 1970’s this is only scratching the surface.
Biologically the definition of a species is a group which can no longer reproduce with another. Unfortunately this definition fails to describe what happens between A-sexual and single cellular species. While sexual reproduction can occur in single cellular organisms A sexual is particularly favored. In this case biologists rely upon what is termed the morphological definition of a species. A morphological definition defines a species via similar traits and shapes.
Now both of these definitions are only used because they’re currently the best we have without DNA sequencing and they can lead to some faulty conclusions. For example it was largely assumed that Bacteria and Eukaryotes were the only two lineages of creatures, however comparisons between Bacteria revealed another group of what seemed to be bacteria but most certainly weren't These were named Archea and we know they exist because of phylogeny. Archea look like bacteria but are surprisingly more related to us that they are to the common Bacterias.
Phylogeny compares genetic sequences between two creatures and looks for the number of differences. Remember when I said earlier that DNA has an inbuilt rate of mutation? Well this rate is highly predictable and because of that, the number of differences in DNA from humans to a bacteria and everything in between can be traced to their origin much like a game of telephone.
Phylogenetics demonstrated clearly that a large group of what we had assumed were bacteria (mostly due to resemblance superficially) were actually evolved from a common ancestors with Eukaryotes and were in far less related to any known species of bacteria. Thus while the morphological and biological definitions of species are very important to resolve taxonomic differences between species which we have little or no genetic data on (yet) they are almost always trumped by DNA.
Heredity:
What is Heredity? To put it simply Heredity is the concept that our genetics are passed on to our descendants. Hereditability is a key feature of DNA because upon replication DNA has the opportunity to pick up novel mutations. This is particularly why single celled creatures evolve so fast and most have little need for sexual reproduction to speed up this process even further. The first creatures reproduced by a-sexually budding off of one another using RNA as a template for further development. At some point RNA picked up an error, instead of Uracil, thymine was used. This might seem like a big issue, however chemically the two are very similar, and thymine allows the single stranded RNA to do something even more impressive, it allows RNA to form a double helixed structure called DNA.
Organisms began to use their DNA as a source of a base code; this ensured that natural mutations of RNA did not result in such frequent deaths to its host because DNA stabilized the mutation rates of organisms. Along with the other structures within these protolifeforms DNA was passed as heredity from ancestor to descendant.
Thus the central dogma of Biology had come together. Namely that DNA produces RNA which produces proteins and etc. What is the evidence that RNA probably predated DNA? Well for one viruses (called bacteriophages) represent a good example which inject their RNA into cellular hosts hijacking the isolated environment and whatever resources said host has. DNA’s success likely had to do with its ability to resist this invasion as well as serve as a blueprint to recognize foreign RNA particles. This microscopic arms race resulted in an explosion of single cellular life.
Homology:
What is homology? Well to put it simply it’s the study of traits which are similar from ancestors to descendants For example you probably share several homologous traits with your parents who share traits with their parents. Homology explains most (but not all) examples of creatures with similar features. Why do all mammals have five fingers and toes? Homology, tells us that they probably descended from a single organism which also had five fingers and toes. Homologous traits allow us to trace the lineages of larger creatures with much more complicated genomes. Unfortunately while sequencing a bacteria’s genome is very possible with simple electrophoresis and thus we possess a large record of single cellular organisms’ evolution with larger creatures this becomes more difficult. However since the completion of the human genome project this process is becoming more and more frequent and is by far the preferred method.
So can homology be wrong? Yes. Take for example the snake. The snake does not have limbs yet we would expect the homologous traits of land animals all to share the trait of four limbs. Does it make more sense that the snake evolved independently of other land animals or that it lost its limbs? Homology alone might lead us to conclude that snakes lost their limbs because they evolved independently, perhaps from eels or other types of fish. Unfortunately this explanation is unsatisfactory for many reasons, key amongst them is that snakes share almost every trait with reptiles and it’s highly unlikely that another fish would evolve to conquer the land with competition already established. Thus we can conclude a good hypothesis is that the snakes lost their limbs.
If our hypothesis is correct we should be able to find creatures which resemble snakes which also have their limbs. The modern skink is a great example of a creature which seems half way between a snake and a lizard. Most skinks have significantly reduced limbs, are long and some even don’t use their limbs at all to move around. The fossil record shows a similar thing happening millions of years ago with lizards; lizards were evolving to have longer and longer bodies with smaller and smaller limbs. Remnants of these limbs can even be seen in some examples of particularly ancient lineages of snakes, most notably the constrictors which were amongst the first types of snakes to appear in the fossil record. These snakes (even today) still have both their front and hind limbs connected as they would be in an animal with 4 limbs but reduced into tiny spurs. Snakes which evolved later had no spurs at all.
This leads us into the term synapomorphy, a synapomorphy is a trait shared by an ancestor and all of its descendants For example the synapomorphy shared by all mammals is lactation. In fact the name Mammal comes from the term for mammary glands. What is a synapomorphy shared by all Chordates (a type of animal)? A Notochord and a hollow dorsal nerve are shared by all chordates (the familiar type of fleshy animals). Similarly all hominids shared a bipedal posture with an erect backbone which no other animal has, this is a synapomorphy for hominids and these help us define different lineages of creatures.
Chapter 4: Natural selection and Evolution
Now that we understand the background that other scientists do we can finally begin to discuss the concepts of natural selection and evolution. It’s important to note that evolution is not progressive. There is no hierarchy of animals and evolution does not have the goal to ‘produce’ humans from bacteria. Evolution’s only goal (if you want to call it that) is to produce an organism capable of surviving and evolution’s mechanism to do so is mutation. Not all mutations are evolution but all evolution requires mutation.
What prevents evolution from creating a poor mutation? Well nothing does. In fact many different mutations are horrible mutations which lead to poor side-effects. These side-effects have the result of either killing off the offspring outright, or producing an inferior descendent with traits that are quickly driven to extinction.
This process of dying off of the those animals with poor traits is called natural selection. For example if you were to alter one base pair in DNA you could alter the amino acid it codes for, if you alter the amino acid that it codes for then you could produce one of two effects, either a protein which does its job worse or a protein that does it better. A great example of this is mutations within the DNA responsible for coding for hemoglobin in blood. In humans these mutations frequently result in embryos which cannot live, less often, the embryo remains livable but the blood oxygenation is very poor leading to tissue damage and other side-effects.
On the other hand antibiotics work by interfering with the biological processes of certain organisms and are reliant upon the organisms’ traits to work. If the organism loses this trait it can then avoid the effect of death. In bacteria, a single point mutation can cause a new protein to take the place of the former protein rendering the bacteria and it’s descendants entirely immune to that type of antibiotic. Without the antibiotic however the native type of bacterium in most cases can out produce the mutated individual.
What type of mutations then are good mutations? Usually mutations which affect the basic machinery of cells tend to kill their hosts. For example you and a bacteria share many different enzymes proteins and other structures in common. Why is this the case? Well simply put these very formative traits are important whether you’re a bacteria or a human and to alter them causes life to fall apart. This means that certain types of mutations will almost never occur. For example the protein responsible for translating RNA into protein is nearly the same in all life forms.
As multicellular life appeared the basic machinery that drove the life in the single cellular descendants remained intact.
The first multicellular life appears in the fossil record about 540 million years ago. These organisms represented very simplistic forms of life. In fact genetically we know that their bodies could be reconstructed with a few very simple biological commands. These organisms grew simply by stacking more and more cells on top of each other in a fractal pattern. They were very thin and absorbed most of their nutrients directly from the water around them similar to how a modern tape worm would absorb nutrients in your gut except these lived in the ocean.
This phylogenetic tree represents the tree of life with only organisms who have been sequenced:
This more basic phylogenetic tree represents the relationships between all known organisms within 98% certainty.
The following phylogenetic tree represents the DNA relationships between different species of animals allowing us to trace with 99% certainty their relation and evolution.
However this form of life was presumably a dead end because these creatures all died out. Unable to move, they were easy prey for early colonies of single celled creatures called Choanoflagellates. Choanoflagellates are very simple single celled protists, these protists have a ‘mouth’ and a cilia which they spin to create a suction. This suction pulls water and particles towards them and filter out useful particles to live they also allow them to move. The key feature of choanoflagellates is that their mechanism of feeding works better the closer they are to other choanoflagellates, which is to say, if you can only suck so hard, with your friends you can suck much harder. These first colonial protists appeared about 640 million years ago.
From these creatures (or creatures very much like them) sea sponges evolved in the water. These sea sponges, along with early forms of fractal life shared the sea floor. However the sponges were unique, although just like choanoflagellates they could ‘survive’ as single cells when left to their own devices they produced collagen and glued themselves together. These glues formed channels which allowed the similar cellular structure to in turn filter feed even more effectively. Sea sponges are quite impressive animals and we know they are animals because they share 24-isopropylcholestane with all other animals which makes them in turn true animals.
Sponges had no particular orientation and like modern sponges could grow in innumerable ways and shapes. They have only one cell type, which we can call a germ layer. What triggered the first multicellular life? It seems that nutrient abundance allowed single celled organisms to proliferate at an extreme rate, some single celled organisms began to work together with the nutrients available finally providing enough energy to do so. The reason for this was a phenomenon called snowball earth in which an iceage which extended from pole to pole covered the earth. During this time only very simple organisms were able to persist but the concentrations of carbon dioxide were massively increasing as volcanic activity generated more and more, including organic compounds which could then be utilized by the trillions of creatures in the oceans.
The next big leep in evolution took place when sponges duplicated a large portion of their genome. Before their genome only coded for one type of cell, however by duplicating this section two types of cells could be created. This allowed for the first time animals which had an ‘inside’ and an ‘outside. Called germ layers, the first eumetazoans had evolved. The first eumetazoans specialized into what we know today as cnidarians or Jellyfish. Cnidarians compose corals as well as jellyfish. These new creatures were composed of a non living gelatin like substance sandwitched between two types of cells, one external and one internal.
Competing with the sponges which preceded them they drove many types of creatures extinct including many lineages of sponges. Only the sponges which were most resilient survived the new animals. Soon cnidarians gave rise to ctenophore which are jellyfish like creatures lined with cilia. Unlike their jellyfish relatives who moved very slowly tenophores were capable of fast movement. Still most creatures at the time were filtering organic molecules from the water around them.
Another group of animals existing at the time were placozoans which means literally flat animals. These animals were composed of a thin layer of cells working together which crawl along flat surfaces. Regardless these animals were very simple. A study of phylogeny indicates that all animals today evolved from ctenophores into a large group we called bilatera which means that the animals had bilateral symmetry (or a front and back).
Bilateral organization of animals allowed them to concentrate sensory organs on the front which was necessary as increased speeds and abilities are simply much more energy consuming on a radially symmetric creature such as a jellyfish. Bilaterially organized animals evolved into two groups, the Protostomes and the Dueterostomes which literally translate into mouth first and anus first. Bilateria had another type of cell that their radial ancestors lacked, which was the result of another duplication event in the genome. This third germ layer gave all animals which came after it the three germ layers which in turn make up every body including our own.
During the embryo development of Bilateria a stage called gastrulation occurs. This is where the early cells which have merely increased in number up to this point (but not in size) organize themselves. Mesoderm goes into the middle, with endoderm lining the inside and ectoderm lining the outside of the developing embryo. In doing this they create a pore within the cellular mass. In protostomes this pore becomes the mouth, in deuterostomes this pore becomes the anus.
It key to understand in all animals endoderm, ectoderm and mesoderm form the same types of tissues. Ectoderm forms our skin and nervous system (which is derived from our skin) Mesoderm forms our musculature and organs. While endoderm forms the lining of our digestive tract. It’s easy to see then how radially symmetric animals like jellyfish only had endoderm and ectoderm, an inside and an outside.
This tube within a tube within a tube organization is the same for every animal on the planet. What triggered this development? Well the genetic explanation is key but the diversity that came with it was probably triggered by the first true predatory animals which appear in the fossil record during the Cambrian explosion in which all modern animal clades formed. These animals introduced the need for a variety of different innovations in order for other animals to survive. Armor, spines, tentacles, fins, mouths parts and etc all evolved during this time.
Protosomes evolved into three distinct lineages, the platyzoans which are essentially flat worms. These worms lack a coelom which essentially is a fluid filled cavity for the formation of organs or use as a hydrostatic skeleton. Because of this they tend to be extremely flat. The ecdysozoans shared an exoskeleton or cuticle which must be shed to grow and a true coelom and lastly the lophotrochozoans which all share a form of larvae which are ciliated and move before growing larger and also have a coelom.
Obviously athropods all have an exoskeleton and spiders, sea scorpians, nematodes, crustaceans shrimp and etc. Represent the modern descendants of this group. For a time the arthropods represented the most successful and dominant group on the planet with sea scorpians reaching up to two meters in size. Arthropods also have another less obvious advantage; the same structures that allow them to move, on the sea floor also allow them to move just as well on the surface. As expected the first animals to colonize the land were arthropods.
The other important animal group was lophotrochozoans which formed the lineages of molusks, snails, and a variety of types of worms (of which earth worms are a part of). Lophotrochozoans also evolved hard shells excreted from their mantles (a structure shared within the group) these first sea snails were able to move upon dry land by sealing their shells to prevent drying out. Eventually both the ecdysozoans and the lophotrochozoans had evolved lineages which no longer required an entirely moist envivornment. This is easy to see as though an earth worm requires moisture to stay alive, in waterlogged soil the worm will drown unable to absorb the oxygen which is abundant in the air but far less so within the water.
At the same time as protostomes were evolving and taking over the world a smaller group of organisms was scratching out an existence under the shadow of the dominant species, the deutersomes. These creatures were odd in that the pore within their gastrula formed an anus instead of a mouth with the mouth parts forming later. These animals developed their coelom differently as well pinching it off from the tube formed by the endoderm.
Instead of developing a hard external skeleton these creatures relied upon a stiff structure called the notochord with muscles running down both sides and a relatively soft skin. These creatures went on to form the lineages of echinoderms (sea stars), chordates (all vertabrates) and acorn worms.
Since it’s the vertebrates that we really care for we’ll continue down that lineage. Keep in mind every lineage is evolving independently in parallel with other lineages. While the ancient ancestors no longer exist descendents of almost every major group still do exist which present an excellent case study of what anatomy looked like as well as what changes to that animal would cause.
What was happening to the DNA at this point? Well DNA in the eukaryotes had grown extremely large and condensed; to save room DNA was wrapped into complexes called chromosomes which allowed all of the genetic information which in turn built the blueprint of the animal to be stored. For example, most of the same genes are found in humans and in fruit flies, but not all of these genes are activated in the same way; further humans have more complicated mechanisms because of their larger bodies. As a general rule the larger the organism the more complicated it’s DNA has to be. But this isn’t in producing entirely novel structures, only in organizing those structures in a novel way.
The largest explosions of life happened in response to evolving new eating methods or ways to reproduce. For example the evolution of the Jaw in chordates allowed for the first time for true ‘mass eating’ which is essentially taking bites or pinching off chunks of prey or organic material. The evolution of jaws happened early in chordate history. Good examples of what early chordates probably looked like are the hagfish or the lampreys. While they possess skulls they have no jaw. Thus they feed by latching onto their food via suction or teeth and attempting to tear off chunks of it.
Hag fish and lampreys have seven gill-slits with tiny cartilaginous or bony protrusions to keep them oriented correctly as do their fossil record relatives. Eventually their relatives began to adapt the first gill arch for use as a jaw with the skull literally hinging against the gill arch; this lead to the evolution of sharks and rays.
Early sharks had only six gill slits and smaller lower jaws which weren’t very well suited to predatory action. Predatory action required a more robust jaw and soon sharks adapted their second gill arch as support for their massive jaws. Remember, the basic genes which create either are still in play, the only difference is new DNA instructions telling further development to bring the gill arches together and fuse. In human embryo’s this process can still be seen and when the gill arches fuse improperly it leads to the formation of cleft lips and cleft palates. Our ribs form from the remaining gill arches. Like their predecessors sharks and rays quickly evolved methods to venture deeper and deeper into fresh water. Unfortunately without the supporting structures necessary or a set of lungs which wouldn’t dry out quickly in the air they were unable to make the transition onto land.
Eventually sharks began to calcify not only their jaws but also their cartilaginous skeletons entirely and this lead to the evolution of the first bony fish. Bony fish quickly spread throughout the oceans adapting to all sorts of environments. Their swim bladders also allowed them a variety of control in their ascent and descent within water.
Unfortunately within the fresh water, fish had a problem. If the water dried out the fish quickly died. A group of particularly innovative fish including our modern day catfish began to adapt their swim bladder to gulp air. The air could then be slowly diffused into the dense network of blood vessels within the swim bladder.
These lung fish also shared another key characteristic with their future descendants, five fins (two anterior, two posterior and a tail), in humans today we can count the number of bones in our hand and realize that each bone is also present in some modern day lung fishes who all land animals share a common ancestor with.
As time wore on the affinity to the land grew more and more. Fish had a bony skeleton to support themselves, a swim bladder which they had adapted into lungs and the limbs that all tetrapods that came after them needed. The dawn of Amphibians had begun. Amphibians share many traits with future animals however most of their breathing occurs not through their poorly developed lungs but through their moist skins. With the requirement of a moist skin amphibians were unable to cut their ties with water. However they found a source of food on land which further encouraged them to explore, a huge variety of insects which the amphibians gleefully took advantage of.
As amphibians became more and more at home in dryer and dryer climates their adaptations lead to the evolution of fast growing skin which was designed to dry out and die protecting the living moist inside. These animals were called lizards and they no longer required water. While many amphibians cannot live in water as adults their children all require water to develop. Lizards had developed a trick; a thickening of their eggs had allowed their eggs to retain moisture and allowed their progeny to survive in even dryer environments.
Amphibians were largely restricted to hot or temperate swamps and rainforests. Relying on their environment for warmth however they were unable to colonize the coldest environments. Their lizard descendants shared this disability. Unlike the previous explorers of the surface vertebrates had no limitations on how large they could grow. Only the complexity of their anatomy and their skeleton limited them and without the requirement of the water reptiles exploded in size and diversity. The age of the dinosaurs had finally been reached. Lizards evolved scales, thicker hides, teeth, horns, some took their ribs which formerly had been gill slits and pushed them outside and thickened them into hard bony shells. Others began to add more ribs to their body and lengthened themselves into the first constrictors.
As the age off the dinosaurs continued ever larger more complex beasts evolved and as far as we can tell, though intelligence was possible none evolved. One lineage of dinosaurs, the raptors began to adapt their scales into bristly extensions which in turn became feathers. For a long time the feathers only served as insulation especially on younger dinosaurs although some adapted them even further as we now know. Long before this the first mammalians began to distinguish themselves from early lizards. These protomammals had five fingers and toes, and possessed a particularly important trait, the existence of enamel on their teeth.
Enamel is an extremely hard dense form of the tooth which is no longer alive. This allows a huge amount of force to be placed on the tooth before it cracks or breaks. Lizards and fish replace their teeth constantly but early mammals had stumbled upon a trick that allowed them to keep their teeth, and more importantly crush and penetrate substances no reptilian or fish tooth could. These early mammals specialized in consuming seeds from gymnosperms and crushing the hard woody plant substances. Their tooth enamel and formation of a mammary glands allowed quick production and evolution. Soon mammals covered every inch of the earth, living rather quietly under the foot of the giant lizards.
Mammals developed keen vision and to deal with larger predators enormous brains. However their excessive requirements for energy kept them smaller and no mammalian large predators were able to evolve as large mammals were easy pickings for the even larger dinosaurs. It took a massive extinction event and another 8 million years for mammals to get their chance. However the millions of years spent evolving and adapting had made these first mammals into extraordinarily smart, creatures who could survive even in the coldest climates.
After the massive extinction event which wiped out the dinosaurs and produced the enormous crater in the Yucatan peninsula mammals were amongst the first to recover. Their only competition was the surviving members of the raptors and many smaller reptiles. The Raptors quickly re-established their dominance and became known as the terror birds. Enormous bird like predators which could reach over 3 meters tall. It seemed that the mammals had lost their chance at dominance for good.
The mammals had another trick. Up to this point mammals had evolved to lay the same amniotic eggs as their cousins the reptiles. In an obscure part of the world which is now modern day Australia the mammals stumbled upon a system of reproduction which allowed even more rapid growth of populations. Though lizards and fish both had long ago evolved ways to give live birth and many animals retained their eggs in pouch like structures (like today’s platypus) the combination of warm bloodedness, ability to eat anything and large brains allowed the marsupial mammals to explode. The first top predatortory mammals had appeared on the planet.
With the large brain size and advantages in development a large creature which resembled somewhat of a combination between a rat and a cat began hunting in groups. Though only a couple of feet large, the combination of superior teeth and hunting tactics quickly drove the terror birds to extinction. Although some terror birds still survive today (such as the emu and ostridge) the dominant animals soon became the mammals. Soon the marsupials were replaced by even more virulent placental mammals (all lineages starting mostly with rodents) in all continents except Australia which had become isolated. Of these placental mammals some crawled into trees, these tree shrews began to evolve traits which helped them live in the trees and hunt their primary food of insects and fruit. Some became bats and grew wings, and some got a lot smarter at acquiring food.
Forward facing eyes and the ability to remain upright clinging to the trees was critical to these early treeshrew like species and they soon evolved into tarsier like creatures. These creatures further evolved into the modern lineages of simians, lemurs and tarsiers. Simians quickly became successful across the entire world spreading from one corner to the other. Simians then split again into new world monkeys and great apes (the remainder representing old world monkeys), the great apes lost their tail and some of their agility in the treetops but they began much stronger and much more intelligent than their new world cousins. Soon the apes split again into the great apes and the hominids.
The hominids much like the great apes had lost their agility that allowed them to so effectively live in the trees. They became primarily ground dwelling forming nests and hiding in the treetops. Their large range necessitated an even larger brain and soon their bipedal movements necessitated the fusion of the foot bone. Unlike apes which walk with knees bent, hominids catapulted their legs over one another like stilts essentially walking as a controlled fall. This allowed them to walk indefinitely and they quickly migrated across the world.
In an obscure corner of Africa, the rift valley one type of hominid we refer to in general as archaic humans (which include for example Neanderthals) evolved to deal with the wide open grassy plains of Africa. Unlike their archaic brethren which were suited more to life on the forest floor, the first modern humans were relatively thin, and weak. They required little sustenance in comparison to their brothers. However they possessed an extremely developed culture which speaks of their great ingenuity. Quickly modern humans supplanted the remaining archaic humans which had been slowly dying out due to climate changes.
Of course it wasn’t so easy for modern humans either. We very nearly died out ourselves due to climate changes and our genetic variation tells us that at some point our numbers had dwindled to as few as 1,000 breeding pairs. Those that survived possessed the most successful traits hominids could create, representing a balance between strength and efficiency, and wrapping it all in a extraordinarily intelligent package. There’s some evidence that these modern humans interbred with archaic humans but by the time this had happened modern humans were so numerous as to entirely bury the contribution of archaic humans to our legacy.
Fast forward to about 10,000 years ago when farming became common and humans began to evolve affinities to consumption of hemp (one of the first cultivated plants) as well as began milking the first domesticated farm animals. At about 5,000 years ago most humans had acquired the ability to digest milk throughout their lives which is typically shut off via a genetic switch after weening. As food became easier and easier to obtain our attentions turned elsewhere, and finally to understanding our own origin.
All in all the evidence for this is provided by phylogenetic comparisons, the fossil record and modern understanding of DNA. Evolution is a fact, pure and simple and debating it is more than a little foolhardy.
Chapter 5: Development of the Germ Layers and Embryogenesis:
So how do cells differentiate and how can evolution on the genetic level result in the production of new creatures? Well it all goes down to how cells come together, a rather simple alteration of the genes responsible for building our bodies can result in a massive morphological difference.
Essentially in embryonic development of humans there's a few stages within fertilization. The process begins with the production of gametes, gametes are 1n cells meaning that at every loci for genes they possess 1 allele instead of two as they need to in order to replicate. When sex occurs sperm cells begin a journey through the folds and intricacies of the female anatomy up to the Fallopian tube where no sperm may make the journey successfully (why men with low sperm counts have trouble getting women pregnant). When and if the sperm do make the journey successfully they burrow into the egg at which point a chemical reaction occurs within the egg which calcifies the surrounding egg and places amniotic fluid between the body of the egg's first cell and the shell further ensuring the egg isn't fertilized twice. If the egg does become fertilized twice, instead of having the normal number of 46 chrosomes composed of 23 from the sperm and 23 from the egg, a double fertilization may result in 46+23 chromosomes. Because the structures of our cells do not have a way to deal with this they usually fail at the outset although a few disorders are known to occur because of the rare exception.
Now our first round of mutations occurs both at the formation of these sex cells which occurs before birth for women and continuously in the testes of men. Mutations in meiosis can result in any of the following manipulations of the genetic code:
A deletion of a gene can occur at this point:
This occurs as a normal part of meiosis and the reason it occurs is because genes are not strongly attatched to the centromeres, the result of this is the gene falls off of the genetic code which in turn can no longer code for the genetic product it makes, although the DNA may still technically be present within the cell if it's not attatched to the chromosomes our cells have no way to make use of it and upon further splitting of cells the DNA will not be duplicated meaning future cells will not have it at all.
Genes can be duplicated at this point:
This occurs because instead of separating into their respective sides pulled apart by centromeres, like a deletion event the centromere on one side of the division has a poor attachment to the gene. This results in the creation of two daughter cells, one which has the gene deleted from it, and one which has a double copy of it. If the double copy cell becomes the egg or sperm then the new embryo may have a duplicated gene.
I for example have a type of duplication of my FOXO3 in which the gene does not align properly. In many cases this would be a bad thing but in my case and the case of many centarians the gene product actually functions much better at doing what it's supposed to do which is cleaning up extracellular and perhaps intracellular products. Unfortunately because of this misalignment the gene duplication itself is not heritable to my children meaning they have a similar 1 in 100 chance of receiving the gene.
More importantly duplication events can be very beneficial and heritable. For example the reason we have 3 color receptors in our eyes and fish have 2 is because our genome duplicated the gene responsible for color vision. This produced an excess of products which in turn allowed the same cells to detect light at lower and higher energy levels. Which instead of just seeing blue and yellow colors we see green, red and purple colors as well. This can occur in any creature and in the mantis shrimp this duplication has occured as many as twelve individual times meaning they can also see microwave, infrared ultraviolet and even radiowave electromagnetic radiation. Very useful on the bottom of the seafloor.
Genes can invert their placement on the chromosome:
This may be a large deal especially if the product that the gene codes for accelerates or slows the product of a different gene product.
Genes can migrate or translocate to another chromosome. This can change in turn how the genes are inherited and can increase or decrease their ability to change independently of other genes.
Now there are mutations on the DNA sequence level as well as on the genomic level. These mutations fall into four categories:
Deletion. Deletions tend to be some of the most influential point mutations. For example if the genomic sequence is translated into RNA which reads C-G-G, A-U-G, A-G-G (remember rna is the mirror image of the DNA with Uracil instead of thymine) which codes for the amino acids Argenine and methionine suffers a deletion event affecting the second G of the code. This in turn shifts the frame of reference back 1. Now the genetic code reads CGA TGA GGX (X representing whatever comes after AGG) CGA codes for Argenine as well which is beneficial, because there's 64 total combinations of 3 letters versus 20 possible amino acids which means several amino acids are coded for twice this means this mutation was nullified by redundancy. However UGA does not code for a protein (typically) and insteads serves as a stop command for the translation of the gene. If the protein is 400 amino acids in length it's just been cut to 1 amino acid. This is a particularly damaging mutation. However the mutation could easily happen towards the end of the gene anyways nullifying it's damaging effects overall.
Insertions. An insertion is when a single base pair is inserted into the genetic sequence. Just like a deletion this shifts the frame of reference over one which can be a particularly bad type of mutation for the same reasons as the deletion events. Now both deletions and insertions may be good changes which actually improve the function of the protein by chance by it's fairly rare for that to occur. Most often the mutations are nullified at this level by stabilizing mechanisms or redundancies.
Inversions are less severe mutations typically because they simply result in the DNA in the genetic code simply switching base pairs, this is a fairly common thing to occur. For example instead of AUG an inversion may change the base pair to AAG which codes for a different amino acid all together. This isn't going to change the other amino acids down the line however so these mutations are more likely than other mutations to be beneficial. As switching out a single amino acid may result in a better protein product or a worse one, however again redundancies nullify most of these types of mutations. An inversion mutation is how most bacteria evolve anibiotic resistance.
Lastly you may have a substitution where instead of inverting the local code a new nucleotide is used all togeher. Thus AUG may become ACG. Similar effects to inversions may occur with these. Here is a list of amino acids and the nucelotides that code for them.
It's important to note that every one of these mutations occurs as a chemically predictable rate. They are not random. Also, when the cells recombine they have another opportunity to go through this cycle of mutation one more time. Which means at fertilization another chance to introduce genetic information takes place.
There's further mutations which may occur in the process of development. These are somatic mutations (which usually result in nothing except aging or cancer) which are not heritable and germ line mutations which occur early in the development of the embryo in the stem cells, which may or may not be heritable depending on where and when they occur.
Now to keep track we've explored gamete formation of sperm and eggs, and the formation of a zygote or a fertilized cell.
The zygote now goes through a process of rapid cellular divison leading up to a process of cleavage. This rapid cellular division does not differentiate any cells, every cell in the blastula may become any other cell in the future child. After about 24 hours the cells have massively increased in number but the size of the blastula is still roughly the same as the single fertilized egg cell.
Cells now undergo a critical process called gastrulation. This is where the blastula cells differentiate into their three respective germ layers. They do this because the egg cell has concentrations of different protein markers at specific poles of the egg. One protein tells the egg which side is the anterior portion and only concentrates on the anterior forming a gradient towards the posterior end, another protein concetrates on the posterior end of the egg forming a concentration gradient towards the anterior end. Other products forms the dorsal/ventral concentration gradients telling the cell which is front and which is back, finally a left right concentration gradient forms.
Using this information the cells undergo their first differentiation into 1 of 3 germ layers. The endoderm, the ectoderm or the mesoderm. The endoderm forms the interior lining of the digestive tract and digestive tract organs. The mesoderm forms our musculature and other organs, the ectoderm forms our skin and nervous system.
It's critical to remember that in the stages of evolution we didn't always have three germ layers and the development of the third germ layer (mesoderm) separates creatures like jelly fish from creatures like worms and cats and humans. Furthermore the development of two germ layers (endoderm and ectoderm) isn't present in even more basic creatures like sea sponges who only have one 'germ' layer. Germ layers are formed in response to hox genes which means their formation is as simple as a duplication of the hox gene. Which in turn allows far more variety in the future creatures the cells are able to produce.
Think of it as a tube within a tube within a tube. I'm going to use origami to explain the concept here. If you only have a paper tube you can only fold or bend that tube in so many ways. If you have two paper tubes you can only fold or bend it so many ways but you can in turn create far more complex structures. If you have three paper tubes you can create fantastically complex structures simply through folding the three layers in different ways. If you cut off our arms (which are folds of ectoderm and mesoderm) we too are tubes within tubes just like an earth worm.
Durring gastrulation the three germ layers must move because they form only in response to top/bottom front/back or side/side. The ectoderm must cover the outside of the developing embryo (less it's skin is on the inside) the mesoderm must be between the ectoderm and endoderm and the endoderm must be inside to create the developing digestive tract. In humans the pore through which these cells move is called the blastopore which as in all deuterosomes develops into our anus. Our mouth doesn't form until sometime later after gastrulation.
During gastrulation two groves form which gradually pinch together through the ectoderm to form a hallow tube on the dorsal side of the embryo. This will become our spinal cord with the anterior portion eventually forming our head and the posterior portion forming our tail. Several folds within the germ layers commence for example at our head region the neural tube undergoes several folds which in term forms the ventricles of our brain.
The final stage we go through is the somitogenesis which in response to locational data created by the germ layers which in turn was created by the initial concentration gradients of the first egg cell more specific organs begin to form. At 8 weeks the embryo is undergoing somitogenesis and begins to look less like a mass of cells and more like an animal of some sort.
The development of structures durring somitogenesis is specified by the formation of hox genes. For example all tetrapods have hox genes which specify the formation of two arms, a tail and two legs. If these hox genes were duplicated in mutation adding another two legs or another two arms is of small issue. However there's an inter-related nature of hox genes meaning that the formation of extra arms or legs is difficult for the body to adapt to without other hox genes helping to make those legs functional. The most simple mutation of hox genes is obvious in those with third or more nipples. This occurs because the hox gene specifies that in X location (marked by somites, germ layers and chemical gradients) make a nipple. Since nipples are very simple structures compared to arms it's fairly easy for this mutation to take place without threatening the embryo itself. The different number of fins in a fish are solely in response to different hox genes. The placement of wings on an insect is due to hox genes. The ears on our head are placed by hox genes. Hox genes are the final stage of differentiation and they in turn kick on in response to time and chemical markers.
For example the reason our brain which has the same genetic code as a chimp's brain is bigger is due to an alteration of the timing gene which activates the hox gene responsible for the fusion of the bones in our head. Because the fusion occurs late the brain itself continues to grow and grow and grow until finally the hox gene activates (at about age 4) telling the skull to fuse and preventing the brain from further developing.
As you can see the organs and functions which unite us with the rest of the animal kingdom form first, those which distinguish us from for example fish have not yet formed and looking at a fish embryo you would find it difficult to tell the difference. Primate eyes differ subtly from other eyes at this point meaning the only real way to tell what creature it is is by looking at the eyes and even then you wouldn't be able to tell much more than whether it was a mammal or lizard or otherwise.
To give you an example of how simple new structures are to evolve here's an evolutionary tree with relation to HOX genes which in turn code for what goes where. As you can see more complicated creatures have more hox genes which are essentially like the steps of folding in origami.
Chapter 6: Diversity of Species and Speciation:
(text limit reached)
Part I
Chapter 7: Links to evolutionary Questions:
The Monarch Butterfly, Flight Migration, Inheritance of Instinct:
Part I
Part II
Part III
Part IV
Part V
Part VI Last quote
Part VII
Part VIII
Homosexuality and the genetic side of behavior:
Part I
Part II
Part III
Part IV Second Half
Part V Explanation provided by Matthias
Part VI
Psychopathy, Sociopathy, and Antisocial spectrum disorders, evolutionary origin:
Part I
Skepticism and response to Fallacious arguments, more information about DNA, abiogenesis and evidence for evolution:
Part I
Part II
Part III
Part IV
Taxonomy vs Phylogeny:
Part I
Genetic Basis of Aging and Progeria:
Part I
Part II
The Genetics of Mutation and Embryo Development:
Part I
Transitional Fossils:
Part I
Genetics at Home:
Part I
Elfdude's Guide to Evolution
Reply With Quote
Originally Posted by mkesadaran
