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No intelligent design, only evolution formed the life on Earth and proofs are everywhere around us

Evolution is the essential power in nature and gives answers to such phenomenons as biodiversity, extinction or speciation of organisms

Theory of evolution is perceived as a big enemy for religion and those who believe that life started in a single act of creation. But how can it get to a point, where it is so controversial that it's almost prohibited to talk about? Because we are talking about a question of faith and opinion, understanding (or missunderstanding and unwillingness to understand) of mechanisms that rule the the world around us. The strength and importance of this theory is so widely underrated, but it is fundamental to realize all the proofs fo it, which are putting the evolutionary theory among the essential knowledge about planet Earth.

There is no need to start a next hot discussion about denying creationism. The data speaking for evolution say a message on their own. Some representatives of Church have already stated that evolution could be an explanation for some of the nature rules and there will be a lot more of them in the future. In this point it is not about religion, but understanding of principles which led to a stunning variety of living organisms and of course, to human.

There was never found a proof, which has contradicted the evolution. The reason why it took so long time to arise a thought in human mind about it is written in our way of thinking about organisms. It was focused only on a form of present time, which acts like an eternal substance. This we call in philosophy essentialism and it exists since the age of Plato. Let's show an example of treating a living organism as a substance independent from time. It could be a sheep. No matter how many languages will describe a sheep, it will always look like a sheep. But imagine that we could move in time 10 million years into the future (or to the past) and because of evolution will our sheep have lot of morphologicaly different features. Nobody would call this animal a sheep animore. Charles Darwin probably wasn't the first human, who found out that organisms evolve, but the power of essentialism and the Church was bigger than the courage of those before him. We know a lot about evolution today and I invite you to read an article about the existence and principles of this important theory.

1. Evolution does not build whole organisms, just following of local rules lead to complicated results

Think about the structure of cell. Every organelle, either with membrane or without it, has its own function. For complicated actions there is a need for more than just one organelle, for example synthesis of some products can not be done just by endoplasmatic reticulum. This material (mostly proteins) are modified in Golgi apparatus and ribosomes and also their secretory pathways leading to a place of using need cytoskeleton. We can find stunning amount of such examples and they are prooving, that complexity of organisms is not done by a creator. Local rules are followed in cells, tissues, organs and finally, populations. Every population in every ecosystem has some structure and one individual is just a small piece in whole dynamics and stability. More subpopulations create a whole population of one species and diversity of species is determining the biodiversity of ecosystems. There is no other explanation for this amazing complexity than evolution. We will find out, why it is so.

The main force of evolution is natural selection. But what does it mean? What is the exact explanation of statement, that whole biodiversity on this planet has not been made by a creator? At the beginning, it is very important to realise, that we see the world from a perspective, which doesn't allow us to notice the tiny and local changes leading to a great modifications. People usually look at ecosystems, populations or organisms and understand them as final versions with best possible design. Leopard, which is for us a beautiful and perfect carnivore, is not a final version and it will never be. The same status is not true for any other organism on Earth. What we actually see every second, is an animal in permanent evolution. This principle was difficult to understand until the boom of new science field occured. Today it is the queen of biological sciences. Genetics.

Before the explanation of genetically based principle of evolution I should explain another mechanism. Every plant, animal, or amoeba, has some kind of body struture. If you think that for every such body there is a plan for creation, you are on the wrong track. Let's imagine a situation. An architect, who will be given a plan for any kind of building will be able to spread it into small parts and then rebuild it. But if you'd have a plan for any organism, you will not be able to reach the form, from which it development started. Every individual of any organism is shaped during the complex embryogenesis influented by amount of genes, their expression in time or their activity location. As we see, organisms are not constructed by an overall plan, but their development is dependent on their regulatory and hereditary mechanisms. Now we can go further into the genetics.

Evolution is not running before our eyes, but runs on the level of molecules. Biological information flows in direction from DNA to RNA and then to proteins. It was always this way. Every organism, as we know, evolved with this information inside, even the viruses contain nucleic acids and a protein cover and they breed when they penetrate into the host cell. Proteins are natural compounds able to create infinite amount of tertiary structures. They consist of amino acids, which together form polypeptide chains. Just 20 of them occur in nature and vast majority of proteins are made of them. Amino acids are coded by triplets of nitrogenous bases in DNA and the order of them is crusial for order of amino acids in proteins. Just imagine the protein with 50 amino acids and think about the stunning amount of possible combinations. Moreover, a big group of proteins has ensymatic function -they catalyze the chemical reaction inside any cell. Two cells with the same chemical composition will develop differently, if there are different active enzymes inside them. After the cell division there will be two germ lineages and eventually two differentiated tissues as their descendants.

The amount of combinations for never ending biodiveristy is increased also by mutations. These are the changes in genetic code caused differently than by segregation or recombination. For example, an error can occur in repair mechanism for DNA replication and such mechanisms are present in every organism. They can fix every mistakes done in the code, but sometimes they doesn't. Every minute and second the bodies of living organisms are also exposed to various mutagenes from outside, but also inside. We know, that there is a group of promutagenes, which became mutagenous just after the metabolic processes inside the living bodies. Every such influences lead to mutations. Now we go back to the segregation and recombonation. The segregation principle means, that chromosomes travell to daughter cells in meiosis and also the copies of genes travel with them (alelles -every of them on the one copy of chromosome). There is also a reduction of their amount to one half, so every gamete gets just one copy of particular gene. Again imagine the endless number of combinations of all genes in one cell. Now we have the term recombination (crossing-over) to explain. Two homologous chromosomes (copies) exchange part of their genetic information during the meiosis and because of that we find an unimaginable amount of variations in descendants. When we now think of the whole statement, it's getting to be more clear. Genes (sections of DNA molecules), which are familiar with lot of changes, are coding the sequence of amino acids, and this sequence is influencing the tertiary structure of proteins, which determines the chemical processes in cells and these processes are responsible for differences in embryogenesis.

The whole machinery of evolution is working this way. It is just obeying the local rules, which at the end give rise to a stunning variability. Very important fact is, that the molecular changes in phenotype (what we can actually see on organisms) are just the tip of the iceberg. The history of every species is coded in its genome and because of that we can now suggest the time of divergence between two species hundrets of millions years old. We call it molecular clock and the whole theory is named neutral theory of evolution. The individual changes in sequences of amino acids and DNA have different speed, but in case of one group and one lineage of organisms they are quite constant. How is this possible? The bigger part of genomes of living organisms consist of pseudogenes, which don't code anything now. There's no transcription or translation in them (they are for example regulatory sequences or intrones). These artefacts are just present as a proof of the history of organisms and before they had their particular function. We know organisms (sharks, crocodiles), which seem to avoid any major changes in their evolutionary history. Is it possible, that the speed of molecular evolution is in their case different? Not really.

Natural selection favor just mutations which have positive influence for organism in its enviroment. What happens, if the mutation occurs in pseudogen (kind reader might forgive me the term pseudogene, intron fits better)? Nothing happens. Functional genes (exons) are just a small part of whole genom in comparison to pseudogenes and even if the mutation is in exon, the phenotype can stay in the same position. Living fossils, such as saltwater crocodile, went through the comparable amount of mutations as the other animal lineages, but none of them became fixated (it means abundant in population and important for survival). Next reason, why the mutation on a very important gene can be neutral is „degenerate genetic code“. The word degenerate has nothing to do with some genetically caused failure. It exactly means, that more codons can code one amino acid. The difference will have no influence to phenotype, but we can see it because of molecular and genetic research methods. It is also connected with preadaptations, which are not functional at the beginning, but then can be very useful for some structures. Of course, they are in lot of examples functional and visible in phenotype, but then can be a start to evolution in a different way.

I return again to word  „degenerate“. It practically means that some „letters“ in genetic code are synonyms. It simply means, that some „letters“ of genetic code are synonyms. As we know, these are nucleotide bases :A (adenine), T (thymine), C (cytosine), G (guanine) in DNA, RNA has U (uracile) instead of thymine. I fact that means, that a change in codon from, for example, CGA to CGG still means one amino acid -arginine. I shall give a very good and famous example now, which is usually wrongly understood. You have probably heard this statement before : „Human shares 98 % of genes with chimpanzee“. This information is absolutely irrelevant. Humans don't share any chromosome with chimps, because any tiny little change makes it different. The truth is this -if we connect human and chimpanzee DNA chains, 98 % of their letters are the same. But it doesn't say anything about whole genes, the sections of DNA molecules. The process, which is used to measure the difference between DNA of two species, is called DNA-DNA hybridization. Double helix of first species DNA is firstly heated into the temperature, which makes the two chains splitting apart from each other. Then we do the same for the material of second species and we can put them together. The genetic code does not see the difference between species, so nucleotide bases will find their complementary partners (A-T, C-G). Now we can measure the temperature, which makes this two-species DNA separated. The bigger the difference between taxons, the weaker the bonds between chains and the lower temperature needed to separation. The alternative method is to sequence both genomes and then compare the differences between them. With molecular clock we can also estimate the time when these two species became separated from each other. In human and chimpanzee case it happened about 6 million years ago. To better explanation -modern people are not descendants of chimpanzees, because in that case chimps shouldn't be alive nowadays. What these two share, is actually a common ancestor and their evolutionary lineages became separated before the time mentioned above.

There is another strange opinion about evolution except the understanding of natural biodiversity as a one system -„suffering“ in nature. If all organisms were created by one creator, he must have been extremely cruel to set the rules as predator-prey and parasite-host organism relationships. How could he create the green-banded broodsac, (Leucochloridium macrostomum), which gets into the host organism (gastropod mollusc Succinea putris) through its gut and then grows to monstrous size and shines in the antennae?  The development cycle ends in the gut of birds, so these bright colours in antennae should attract them. The existence of this organism is harmful for two of other organisms. Another example? Elephantiasis, the result of  getting the parasiting worm Wuchereria bancrofti into the human body. Spirurida, parasitic worms from Nematoda, use as host organisms vertebrates, before this final step crustaceans and insects. The host organism for juvenile stage is mosquito and human must be at first bitten by it. Then the parasite becomes adult in lymphatic system, which may result into massive swellings and inflammation. The examples for suffering in nature are so numerous, they are happening every second you read this article. Predatory animals hunt their prey and their bodies are home for parasites. Natural selection as the main force in nature selects genes and every organism is the system for their replication and passing to another generations. If male lion kills all cubs after winning fight agains previous king of the group, he can now breed with females and pass his genes to next generation. Just we can see this act as a murder. On evolutionary terms, there is just the fight between genes (correctly alelles of particular genes) and their fitness, which makes some of them vanish and others to be fixated in the population. Suffering is the side effect and it is a good proof, that there is no intelligent design. The creator would make the system, where organisms live in the harmony and do not attack themselves. In fact, fear is the one way how to survive. Gazelle, which won't be stressed by the cheetah nearby, would choose the small flight distance and will be killed. The most stressed and first to run will survive.

Mollusc Succinea putris as a host organism to green-banded broodsac (Leucochloridium macrostomum), which makes its antennae shine in various brigh colours.
Human as a host organism to a parasitic worm (Wuchereria bancrofti).
Cruel? No, just trying to survive.
Documentary movies are usually focused on human emotions presented in animals. Animals have emotions, feelings and they react to signals from outside, but trying to say that lion male is cruel is a bad aimed shot. Life in nature is a tuff fight where every moment somebody dies, but also the new life is coming. In fact, it is the genetic information flow, which gives the life some particular direction. It is interesting, how many people haven't already realised that they get in touch with genetics everywhere. Long time before J. G. Mendel human beeings worked with gene pools of animals or plants. You probably know where is my point. In artificial breeding.

In artificial breeding we are transforming the genome of the particular organism and we are focusing on economically important or aesthetic features. It is the positive selection, which excludes unwanted genes and prefers individuals with those we want. Breeders did this very long time, but they didn't know that genes are the important ones in this process, which gave rise to every breed of animals or plants. From on ancestor, wolf, we have after a few centuries of artificial selection big number of dog breeds with various size or temperament. Whether the Siberian Husky, Cocker Spaniel or Chihuahua, all of them are the result of transmission of wolf genes, modifying their embryonic development for many generations to such stage that they differ so much. But their ancestor is still the wolf. Imagine it as the fylogenetic tree -all dog breeds are the descendants of one common ancestor. This scenario is everywhere in nature, but here it happens because of artificial selection made by breeder. It is important to realise, that this way makes speciation of species faster and could be seen as fastened evolution. When we completely exclude endividuals with some features (breeders worked with phenotypes, but in fact they formed the gene pool), they will vanish from the population.

Another information about breeding is important -genes often have influence for more features (they are pleiotropic), or they can create a new feature with their interactions. Moreover, some genes have connected heredity and it happens when they are on the same chromosomes (genetic linkage). I should mention also the quantitative features, which are influenced by many impacts from the enviroment or the genetype. The term „overbreeded“ in breeds of animals or plants is connected with the complicated relationships between genes. It actually means, that if you deliberately breed for some feature, another unwanted one can occur. Because of so many genes with quantitative heredity, the features of organisms are the result of genetic corner-stone shaped by the enviroment. With too much selection the genetic variability vanishes, the rate of some feature can have the negative influence on the other one or because of the genetic linkage the wanted one will form a bond with unwanted one. Breeding for maximum milk yield in cows actually proved to be also the selection for extreme susceptibility to inflammation of the mammary gland. Let me show the example of the complex view of particular breed burened with problems. The English bulldog reached the most torturing level in body structure and because of this these dogs have problems with their eyes, joints and especially, with childbirth. The development of the cranial bones, especially the facial part (maxilla, nasal, frontal) was forced into the extreme shortening by influence of particular genes. Many of bulldog pubs must come into this world by caesarean section, because their big heads won't let them out from the mother. The exact statement about what gene does what is very tricky and that's why for example the dog breeded for agressivity could have also some metabolic problems or strange morphological features as a side-effect. Almost on every breed you will see some side-effects and this exactly is the proof of the complex webs between genes together and also of their relationships with the enviroment.

We can see a stunning variability in nature caused by the machanisms of evolution, but the most important rule is the „trade-off“ rule. In other words, nobody can have everything. If the albatross invests into the long wings suitable for gliding, it may not have enough energy for breeding and because of that the couples raise just one youngster in two years. Another case is, that this flow of energy can come to a point, where the wings will be so heavy, that it would be impossible to take off (apart from the bones also the muscles and overall body plan should be more robust). With this sort of compromise the natural selection forms the organisms to the suitable version for their enviroment. If the too-long winged albatross will spend all its energy on trying to take off or to stay in the sky, it won't have enough energy to search for food and another one with just a little bit shorter wings will survive. So albatrosses have the longest possible wings which enable them to glide very effectively and find enough food to be physically prepared for the breeding season. In artificial breeding the so called border in particular feature is often crossed and it leads to problems such as those in English bulldog.

The English bulldog with a skull formed by the artificial breeding
The wings which are too long are no longer an evolutionary advantage -trade-off in albatross
The evolution could be studied very well on the islands, because the „bottlenose effect“ usually happens here. The small population of individuals colonising the new island is influenced by the decreased genetic variability inside. In the next generations the genes which will be normally on their way out can become fixed in such populations. This exactly leads to a faster diversification -the gene pools are often separated by the geographical barriers (the mountains or a river could be an island on island). The two populations separated by a mountain range will become to a point where they can't interbreed no longer -the genetic distance between them is already too big. The artificial selection does pretty much the same by creating the artificial gene pools islands, because just some wanted individuals are involved in the breeding process.

The genetic nature of the evolution is very much of a complex topic, but the main plot is clear. We will use this knowledge to continue to the second chapter, where I will demonstrate that we can watch the evolution before our own eyes through the organisms influented by the selection pressures and that also the non related lineages could end with the similar adaptations.

2.The natural selection have influence on every organism, now matter how well adapted to their enviroment they are, related or not related, and evolution happens before our very eyes

The freshwater butterflyfish (Pantodon buchholzi) is small in lenght, but amazing in morphology. Its body really encourage to thoughts about creation for perfect using of its enviroment. Pectoral fins evolved to the shape similar to the butterfly wings, ventral fins have extremely elongated fin rays (lepidotrichia) which help the fish to be stable in the same place under the water surface. This animal is amazingly adapted for catching insects falling to the surface and looks like it couldn't be better. But from the evolutionary point of view it is a basal memeber of bony fishes (Teleostei) with basipterygoid joint between basicranium (basisphenoid/parasphenoid and metapterygoid/endopterygoid) and hyoid branchial arch, which is typical for clade Osteoglossiformes. Butterflyfish is perfectly adapted for its enviroment even in the eyes of any evolutionary biologist. But there is no other view of understanding this  fact that evolution. This fish is an amazing prototype of predator feasting on insects flying over the water surface. In fact we there are many other fish species with very similar lifestyle, but they bodies look completely different. Why would a possible creator waste his time to create many more versions of the same animal, in which he proceeded to perfection before? If organisms were created by intelligent design, all fish feading on small insects in the world will be the same as freshwater butterflyfish. But the reality is different.

Freshwater butterflyfish (Pantodon buchholzi) -so well adapted, that it encourages to thoughts about creator
In fact, there are many fish species which hunt near the water surface and they live in a stunning number of shapes and sizes. Just in Osteoglossiformes clade we find more than ten representatives (genera Osteoglossum and Scleropages) which have the similar lifestyle despite their bigger size. Moreover, genus Osteoglossum lives in South America and Scleropages is home to Asia and Australia. In the same ecosystem of tropical Africa the butterflyfish shares the space under the water surface with killifishes (few genera in Cyprinodontiformes). These usually small fishes live also in other tropic regions and they are also bond to the water surface. There are various other examples, such as the archer fish (Toxotes jaculatrix) which is able to shoot on insects above with a small current of water. No matter how different the morphology of these species is, one feature is still the same. Superior mouth. This fact nicely illustrates the natural selection -in non related organism living in the similar enviroment it can lead to same adaptations despite the different gene pools of them. The position of mouth is a very important feature and every species with terminal or inferior mouth would have a trouble to find any food near the water surface.

Killifish (Cyprinodontiformes)
Arowana (Osteoglossiformes)
Archer fish (Perciformes)

Let’s return back to the freshwater butterflyfish. Does its appearance prove that evolution doesn’t happen or hasn’t ever happened in this case? Undoubtedly, evolution happens constantly in all living organisms. Observing any of them, we only see a particular stage of evolution, not the final version of it. An animal or a plant evolves before our eyes under the pressure of natural selection affecting it and it might become extinct or change completely in several million years. Despite of many mutations or other changes, its fenotype can remain almost identical. Creatures like the butterflyfish reached the advanced stadium of adaptation to a certain environment. Studies comparing mitochondrial genomes of butterflyfish population from the Congo basin and a population living in the basin of the Niger river have found amazing differences between them. Sequences of these two populations of one species are different in 15,2 percent (as well as with humans or chimpanzees it is a difference of „letters“ in the genetic code). The estimated time of divergence based on these data is unbelievable – more than 50 million years ago! Despite this inconceivable period of time we are amazed that all the butterfyfish (wheter the one from Congo or the one from the Niger) look pretty much the same. We’ve already built a headstone to understand evolution – so we know now that there’ve been many neutral mutations without an impact on the fenotype and mutations in „pseudogenes“ or better to say intrones. It is so unlikely that a mutation with positive impact on the „fitness“ occured, that it hasn’t happened in 50 million years. Typical examples of this phenomenon are sharks and crocodiles, which haven’t changed according to their fossil material almost at all in 450, respectively 250 million years. There have been large changes at molecular level (what is now used as a molecular watch) but the fenotype went through only slight divergences. The emerge of genetics and molecular biology to the scene itself helped to explain these mysterious events which had been considered to be the missing points in the theory of evolution since Darwin published his work.

We will return to the freshwater butterflyfish in the third part where the position of swim bladder in the group where it belongs becomes an arguable example of evolution of tetrapods (that means also humans). Suffice it to remember the connection with secondary palate on a skull for now.

Evolution causes changes that can be seen in a period of time which humans are not able to perceive. We can only imagine how organisms looked like one million years ago. Nowadays, however, we distinguish enough examples where the speed of changes can be observed in a period of a few years, or even months. Results of the guppy research by John Endler where the coloration of males in an environment with predatory pressure and without it was studied, are well-known. When constructing a shade with guppies and a dangerous predator the coloration of males had become much less prominent in a few months than in a shade without a predator. Simply said, the predatory pressure had a greater impact on guppy males than the sexual selection of females choosing the most colourful males. These particular males were masked the worst and died as the first ones because of their coloration. The males with less prominent colours passed their genes to the next generation. The other shade enabled the males to affect the females with their bright colours because there weren’t any predators at all. The most colourful ones were chosen by the females here and within a few months, there were a lot more bright males in the shade.
The best way to observe evolution is on those organisms which have a very short generation period – that is why we are able to see any important change in a quick period of time in them. It is a generally known fact that bacteria reproduce quickly. So quickly, that they adapt to human pharmaceuticals and become resistent to them. You can experience the natural selection easily in your own home. It is recommended not to interrupt the antibiotics treatment and finish it even though the one feels fit already. If you think about it from a perspective of evolution, you’ll understand why is it so. Eating the prescript amount of medicine you’re lowering the risk of surviving the bacteria and enabling them to become resistent. If you won’t do that, the strongest ones will survive due to the natural selection and the formation of a new, dangerous bacteria patogen is on the way to arise.

3.Fossil records represent an interesting material for enabling us to study evolution and give us an opportunity to understand the genetic history of all living organisms, characteristics without an obvious purpose represent an
evidence of evolution of different lineages from one ancestor.

In previous parts we focused mainly on features positively selected through different selective pressures. But there are also other ones, where we cannot distinctly discover their function. They have no positive influence on organism, but on the other hand, they are not harmful either. In these particular cases we bump into a heritage from the ancestors or structures which had had their functions once, but lost it secondarily. For example if we find characters which appear in humans and lobe-finned fishes we can derive their evolutionary relationships from them and suggest an evolutionary history with a common ancestor. It is important to mention once again that evolution can be clearly proved by observations of recent organisms and fossils are only some kind of exciting guide to understand the past. Looking for arguments against evolution among organisms for which we don’t have sufficient or any fossil material at all is just a mere desperate attempt to confirm a different origin of life than the only one which is scientifically proved. Fossils aren’t neccessarily crucial, but how much incredible information can we acquire from studying them! This area of scientific research is especially subjected to criticism from the creationists and opponents of evolution because it offers an opportunity to use a bit of imagination. Paleontologists and othes scientists, however, mustn’t let the imagination become the headstone of all knowledge, that’s why they follow verified data and try to offer the most probable explanation. There is a great number of complex evolutionary issues based mainly on fossil research, e.g. evolution of birds within dinosaurs or evolution of tetrapods due to moving of their ancestors to the land.

Phylogenetic trees are the best way to demonstrate the evolutionary history of either recent or extinct organisms (here evolution of basal tetrapods as an example)
If we were able to travel back in time and watch evolution of organisms, the whole taxonomic system would break down. We wouldn’t manage to recognize the differences among individual species because we could only find temporal stages with equal and different characters. In which point would we be able to claim that we don’t recognize a galago but a higher primate? In a certain phase
the animal would no longer be a galago but it wouldn’t have all the characters of a higher primate yet. The distance of millions of years that we have allows us to build the taxonomic classification of organisms. That is the reason why we don’t feel desperate when only observing evolution in a continuous view. Genes are passed from parents to their descendants but the role of grand parents, great-grandparents and the generations before them is also important. Instead of emphasizing different examples of fossil ancestors of contemporary organisms (there will be enough space for it in many series about particular groups) it is much more interesting and beneficial to refer to some of the fascinating knowledge from the field of comparative anatomy.

Because of our knowledge from comparative anatomy any discussion about existence of common ancestor of all organisms is now over. There are some, who will say that it is better to use „ almost any discussion“, but the proofs are so numerous that I consider it useless. Study of embryo development in various animals shows that the genetic material is shared among them and only modified. Some sections of DNA are becoming important, some of them are suppressed but there is always a way how to activate them again. The universal genetic code of all organisms consists of 64 codons (three nucleobases are coding amino acids),no more and no less. I will focus on some examples from vertebrates (it will be strange if i wouldn't do it) which really deny the suggestions that only missleading interpretations lead to the evolutionary theory. Let's look for evolution of jaws. Somebody who has never been interested in biology or evolution could look for the photograph of the human embryo with pharyngeal arches as the first stimulus. Where did they come from? They are the heritage from our ancestors. We know, that our mandibula (and in all tetrapods) is descended from the first pharyngeal arch, the hyoid is descended from the second and third one, thyroid cartilage from the fourth. Even our inner ear bones come from the modification of pharyngeal arches and I will carry on with this explanation. There are three bones in ear of mammals -malleus, incus and stapes. They allow them to detect the mechanical waves, sounds, precisely. This stage of evolution is the most derived, but everything started with pharyngeal arches. The first pharyngeal arch was modified in aquatic vertebrates to ossified palatoquadrate and mandibula, after the colonisation of land the development ended it the cartilaginous stage. For the biomechanical function of this primary jaw joint the small parts have still completed the ossification process -upper quadrate and lower articulare. These bones were moving during the evolution of vertebrates and in mammals they ended as the ear bones -so articulare is called malleus and quadrate as incus. And what about stapes? This bone is derived from the second pharyngeal arch, concretely hyomandibulare, which was used in amphibians for detection of sounds. Hyomandibular was the closest bone to the area where the evolution of ear started -with opening a cavity. And it is the spiracle, the opening between the first and second pharyngeal arch, which is homologous with the middle ear cavity. In recent sharks we can still find this ancient structure right behind the eyes and in fossil animals close to the evolutionary lineage of amphibians it is one of the most important features to look for.

Human embryo in 4/5th week of growth. You can clearly see the basal stage of the pharyngeal arches, but they'll soon dissapear. They are not just a coincidence, but the heritage from the ancestors.
Evolution of jaws from the first pharyngeal arch (green). The second arch is modified in tetrapods to hyoid (red). Both of them are involved in evolution of ear bones. In the first picture we can see the agnathan animal with terminal and praemandibular pharyngeal arch.
The visual depiction of evolution of ear bones. Malleus is derived from articular, incus from quadrate and stapes from hyomandibular.

It is impossible not to mention another example from comparative anatomy, which also shows the strength of proofs from this field. Here I speak again about the african butterflyfish and I will show the link between the secondary palate from the second part of this article. Of course, I am not describing the skull of this fish species and I could choose from a huge variety of different fishes for this example. The butterflyfish uses mostly its swim bladder for breathing, but this organ is usually used for the hydrostatic function. It is actually the outpocketing of the gut, developing in same way as the lungs. In all ray-finned fishes (Actinopterygii, butterflyfish included) this outpocketings evolved on the dorsal side of the gut, but in lobe-finned fishes (Sarcopterygii) it was on the opposite -ventral side. Most of the lobe-finned fishes are extinct today, but lungfish (Dipnoi) still breath the atmospheric oxygen with their outpocketings of the gut. Some of the scientist will call these specialized swim bladders as lungs, and they are not far away from the truth. Now we switch to the from the first glance completely different topic, which is the elongation process of the secondary palate in terrestrial vertebrates. Possessing a long hard palate was a very big advantage because the animal could breath and chew its food at the same time. This feature is crucial for mammals -without the long hard palate their babies won't be able to suck the milk without suffocating. The elongation occured widely in the evolutionary history (especially in mammals or crocodiles), but the complete separation of airway and mouth in vertebrates can never happen. Ask why? Because the ancestors of tetrapods (so also mammals) are lobe-finned fishes, not the ray-finned fishes. In all vertebrates with lungs we can see the crossing of upper gastrointestinal tract and airway. In mammals with the longest secondary palate it occurs only in nasopharynx, then the trachea goes ventrally from the pharynx. Vertebrate lungs as the result of evolution from the ventral outpocketings of lobe-finned fish are the very best example of evolution for me. If they have evolved from the same structures on the dorsal side of the body, the flow of oxygen and income of food could be separated in vertebrates. It will be cleary far more easy to create the terrestial vertebrates again, every creator would do that.

Following the evolutionary pathway can give you the answer to the question about the origin of terrestrial vertebrates.

Thanks to the fossil record it is possible to seek for the shared structures in extinct and recent organisms. If we include also the knowledge from the comparative anatomy, we get a complex view on the modification and evolution of the same genetic code for all organisms on the planet. In the human embryo we can see our fish ancestor with the pharyngeal arches, fish body and interdigital webbing. In the last, fourth part will be focused on the fact, that the common origin of studied organisms can be found even it the position of continents and in the laws of nature on our planet.

4. The continental drift and basic laws of chemistry and physics on planet Earth provide another proofs of evolution

Only in 1912 the theory of continental drift was suggested and it provided a completely different perspective on the distribution of biodiversity on this planet. Gradually it was completed by the theory of plate tectonics and thank to these we now know much about the movement of the continents and dynamics of the Earth mantle. On the surface of the planet is lithosphere, which is broken up into tectonic plates because of the moving astenosphere under it. Tectonic plates approach each other or move away and this process creates mountains, ditches, earthquakes or vulcanic activity. The astenosphere is much more labile than litosphere and has a higher temperature. If we reconstruct the movements of the continents, which are parts of the tectonic plates above the sea level, we can include also the geographic data into the fylogenetic analyses. Until the Triassic period the only continent on the planet was supercontinent Pangaea. It had of course a huge effect on the evolution, which lacked every island effect of diversification of new forms. Before approximately 200 million years ago the Pangaea started to break apart to more continents because of the movement of astenosphere under the lithosphere and it was a trigger to the diversification and speciation. Before the Triassic there were also continents and even one supercontinent (Rodinia) and it became clear that continents are moving in two phases (they are all together as supercontinent and then they break apart). Continents, as we know them today, will form one supercontinent in the future again. This distribution of landmasses is a result of incredibly complicated process and it had a big influence on evolutionary process.

The disintegration of Pangaea took millions of years. Here we can see the distribution of continents during Precambrian, Carboniferous, Jurassic and Cretaceous period.
Tectonic plates and their recent position. They are constantly moving and have impact not only on the formation of the landmasses, but also on the distribution of organisms on the planet.

These basic facts are enough to explain the evolution of organisms according to their geographic distribution. There are numerous examples and one of them is the origin of the modern human in Africa. Why not from the Europe or Asia? Because the oldest fossils of the human evolutionary lineage were found in Africa and these ancestors started a journey to the other parts of the world. But how could they travel to America, which was not connected with Africa or Eurasia? Human foot stood on the american land long before the first boat existed. Thanks to the decline of the sea levels approximately before 25 000 years the Bering Strait vanished and this area became a bridge between Asia and Northern America. Humans and animals colonised a new continent. Approximately 3 million years ago the connection between South America and North America was formed. Until this moment the organisms living on the southern landmass were evolving without any pressure from colonizers, but this has changed and lot of species have become extinct. These and other similar scientific data are a result of study of fossils and comparative work based on the position of landmasses in particular period. If any fossil was ever found in the wrong geological layer (say dinosaur from carboniferous), the evolutionary theory would have a big hole right inside. This has never happen and what can convince somebody to trust that it can be true is for me incomprehensible. But let me explain one important difference. Dinosaurs (of course non-avian) became extinct 65 million years ago after the collision of Earth and asteroid, which landed in the area of Gulg of Mexico. Pterosaurs, ammonites and other organisms vanished too and their fossils can be found only in the older layers. But what if a dinosaur fossil was found in the Eocene layer? It would mean, that our understanding of dinosaur extinction was not right, but it doesn't contradict evolution. Dinosaurs lived before and some species could survived (but hardly anybody beleives in this) the massive extinction. The other thing is to imagine finding a dinosaur fossil in the Carboniferous layer, when the evolution of reptiles only started -this would be a disaster for the evolutionary theory. No dinosaur could live in this period and it would be a jump above many million years of evolution. But trying to find such a proof is truly vain.

The life on planet Earth is possible only because of the specific conditions, which differ from the ones on the other planets. Just say, if there wasn't any rotation around the Sun and around the Earth's axis, one half of the planet would be too hot, the second one too cold for life. It is possible to cut through many topics from physics and chemistry, but probably the most important is the existence of the main engine of life -energy. The only source of energy for organisms (if we exclude some exceptions living in the extreme enviroment at the bottom of the ocean floor next to the volcanic pipes) is the energy of photons coming from the sunlight, which is transformed to the chemical energy by plants. Creationists often speak about the denial of second law of thermodynamics by evolutionary theory and that live matter could not go „against the flow“ and face the entropy of nonliving matter, which produces the disorder. But thanks to the perpetual flow of sunlight there is always energy and organisms can temporarily (until their bodies get stale and die) fight agains the disorder and maintain their homeostasis. Green plants and algae outnumber other organisms (heterotrophic) by ten to one and it is not an accident. All the energy is gradually used on different levels by heterotrophic organisms and on every stage of this chain there is a loss of it in the form of heat. Without energy gathered from photosynthesis, all the ecosystems would crash and this will have a direct impact on the composition of atmosphere. And the atmosphere was very different before the autotrophic organisms evolved, especially the amount of oxygen was much smaller. But how has the life evolved and how could the first tiny algae with chlorophyll for gaining energy from sunlight emerge?
The origin of life is estimated to happen 3,8 billion years ago. It is only an estimation and we will never know how accurate it is. Anyway, finding of carbon isotopes from this age sends a clear message -its nonliving origin is impossible. We also know, that in this time there was a primary ocean where the organic substances were formed from the anorganic ones. The oldest organisms are 3, 55 billion years old and they are the irrevocably proofs of evolutionary theory, not the creationism. The cyanobacteria found in the stromatolites in Australia didn't need the oxygen for their life, just water, carbon dioxide, nitrogen, a few minerals and the sunlight. But for the functioning photosynthesis they needed proteins and we have already spoke about their importance. The most common protein on Earth is the enzyme Rubisco (Ribulose-1,5-bisphosphate), which is used by plants for the carboxylation of carbon dioxide and also during photorespiration, when it bonds with oxygen. Thanks to cyanobacteria and their processes inside the amount of oxygen in the atmosphere was gradually increased. But how could the enzyme (protein), which allows this, occur? The experiment of Stanley L. Miller, which has shown the formation of amino acids from the anorganic substances in the enviroment of elementary laws of physics, gives the way to the answer. All 20 of the amino acids usuall in the nature were formed only from water, methan, amoniac and hydrogen in the closed system of flasks connected by tubes after one week! After the death of S. Miller (2007) it was shown that their number was even higher -25. The enviroment on Earth 3,5 billion years ago was simulated and because of that the water in the first flask was warmed up and then evaporated, in the second flask there was a simulation of flash by two electrodes. Next to come was a condensation and move to the first flask again, which was constantly repeated. If such important amino acids can be formed from anorganic substances, there is no reason to speculate, that cyanobacteria had a source of clinical enzyme Rubisco for their photosynthesis. With the energy gained from sunlight there were the possibilities for the heterotrophic organisms and evolution could start to be faster. No matter how long ago have these organisms lived, just the existence of the findings from Australia should lead to the doubting about relevance of the theory of creationism. Nobody can be sure about the origin of life, but the clues are all around us. A big progress has been achieved since the experiment of S. Miller and new hypotheses have been proposed. The one of the most precise is the hypothesis about origin of life in the small tubes of hydrothermal springs made from sulfur, iron and nickel, where the proton gradient caused by the interaction of cold ocean water (acidic because of carbon dioxide) with the alkaline pipes enabled this system to create chemiosmosis and to produce energy. Also the most important process in the cell physiology could evolve in this enviroment -Krebs cycle (today we know that it is capable of reverse flow with the production of organic matter). If this realy happen this way, or in the primary ocean, we will never know. The important thing is, that despite the incredibly long time, which has passed since the origin of life, we are capable of discovering and putting together the pieces and processes essential for life and prove that our assumptions can be tested in reality. 

The scheme of experiment done by S. Miller showing that amino acids can be formed also from anorganic substances in some conditions
The stromatolites in Australia -the oldest evidence of life on Earth
To conclude, it is important to return back to the previous paragraph. I mentioned the possible formation of proteins also from anorganic substances, but they are alone not enough for life to flourish. But why? Proteins are capable of forming into huge number of tree-dimensional structures and they catalyze the specific chemical processes as enzymes, but they can't replicate themselves. The basic instrument of natural selection for survival of organisms is the command „replicate“ coded in the nucleic acids -DNA and RNA. Until the replication and therefore a sending of genetic information into next generations have occured, no natural selection could have existed. The main source for replication among recent organisms is DNA, which is very good at replicating, but can't form different three-dimensional structures. Neither proteins nor DNA could alone enable the evolution to happen, but we have forgotten another one player -RNA. Contrary to DNA, RNA can replicate (although not so quickly), but can also form the three-dimensional shapes functioning as enzymes. The theory with name „RNA world“ puts only RNA to the position of important component, which should have (and still has, because these features were studied recently) had the potential of replacing the DNA-proteins system in the first stages of life evolution. The question of life origin is a problem, which will not be solved, and that is because of one important reason. The existence of life hasn't been proved on any other planet apart from Earth. What is the probability that life really exists somewhere else? The processes, which happened 4 billion years ago on our planet, were the extremely rare ones and it is very probable that nothing like this took place in the vast space, which is impossible to imagine for us. If we knew directly, what has happened in that time, it would be logical to expect the existence of life on many other places of the universe. Despite the fact, that we will never know, we have scientific data able to find the potential way of life origin in the unfriendly conditions. Life was not created from nothing. Some tiny and small steps must have happened, heading for the bigger units, which after millions of years ended as organisms so unique for us, that we think about some creator as the main force. I came to the end of my story of evolution. But in fact I am again in the beginning, at local rules forming the far-reaching changes.
The evolutionary theory separates. Needs a big attention. Encourages to the desire for knowledge and understanding of principles. Describes the complexity, which is truly amazing. It is different from any other theories about the diversity of life on planet Earth in many points, but one of them is crucial. This theory gives answers to our questions (except from the question about origin of life, as I explained) in at least sufficing way.

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