Evolution
Forms, Genes and Embryos

The Evidence for the Theory of Evolution by Natural Selection

DNA


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Classification of Animal Features

When animals are classified using features they possess, a pattern is formed. This pattern is called a Nested Hierarchy. Similar patterns are formed when plants are classified according to form and features.

Animal Features

In the example above, we classify animals by the features they possess. A feature that appears in a box will also be possessed by all the animals within the smaller boxes. Examples of animals in each box are in the yellow coloured rectangles to the right.

The outer box contains all the animals - so, no plants, fungi or bacteria - they, too, can be classified in a similar way.

The second box contains all the animals that possess vertebrae (in other words, a backbone). This includes all Fish (there are three types: the Jawless Fish, Cartilaginous Fish and Bony Fish), all Amphibians, all Reptiles (both living and extinct), all Birds and all Mammals (again there are three types: Egg-Laying Mammals, Pouched Mammals and Placental Mammals).

Animals like sponges, worms, insects, molluscs and starfish do not possess a backbone so appear only in the outer box, the one labelled Animals.

The third box is a subset of the animals with backbones. These are creatures with jaws, bilateral symmetry and paired appendages. These are the Cartilaginous Fish (like sharks and rays), Bony Fish, Amphibians, Reptiles, Birds and Mammals.

The Jawless Fish (like hagfish) have vertebrae but no (lower) jaw so appear in the second box (labelled Vertebrae) in the above diagram.

The fourth box contains animals with digits (Amphibians, Reptiles, Birds, Mammals).

The animals in the fifth box practice internal fertilisation when mating and reproduce with an amniotic egg. The amniotic egg contains a liquid sac so it can be laid away from water. Internal fertilisation allows fertilisation on land. Both of these features are necessary for living on land. The animals in this box are the Reptiles, Birds and Mammals.

Within the sixth box are animals able to keep themselves warm internally - they are warm blooded. Only Birds and Mammals have this ability.

In the seventh box are animals with hair that nourish their young with milk. These are the three types of Mammals (Egg-Laying Mammals - or Monotremes, the Pouched Mammals - or Marsupials and the Placental mammals).

In box eight we include all the animals that nourish their developing young with a placenta. These are the Placental Mammals.

Finally in box nine we list all creatures with an opposable thumb. Only a single order of Mammals possess this feature: the Primates, a group that includes humans.

Note that humans are included in all the boxes because they are animals, they have vertebrae (a backbone), they have a jaw and paired appendages, they have digits (finger and toes), they mate using internal fertilisation and raise the embryo in an amniotic sac, they are warm-blooded, they have hair and nourish their young with milk, the foetus develops with a placenta and they have opposable thumbs.

The above pattern is called a Nested Hierarchy.

The nested hierarchy based on form and features is a mathematical model that indicates a family tree relationship. It allows animals (and plants) to be classified into groups with shared features (species, genus, order, class, phylum, etc).

The above classification can be explained by the Theory of Evolution with its branching pattern of common descent which provides a logical basis for classification.

An attempt to classify unrelated items like motor vehicles would not generate a nested hierarchy because different vehicles groups are created independently of each other. There is no family tree involved.

The nested hierarchy indicates that vertebrates are descended from a single ancestor that developed a backbone. All of its descendants have inherited that feature. One backboned creature developed a jaw and all of its descendants have inherited that. The amniotic egg developed in a reptilian ancestor. This was then passed on to its descendants: modern reptiles, birds and mammals. And so on.

This family tree also implies that mammals must be descended from reptile ancestors which, in turn, are descended from amphibians which themselves are descended from fish-like creatures.

This family tree has been known for centuries. Several biologists have independently come up with the same classifications. Over 2000 years ago the Greek scientist, Aristotle, classified dolphins as mammals because they gave birth to live young with a placenta.

Animal Descent
Chart showing animal descent with features branching off to form whole classes and orders.

Some creatures are clearly links between two different groups of animals.

The Platypus has hair and warm blood like a mammal. It lactates to provide milk for its young (also like a mammal) even though it has no nipples. However, it has a single reproductive and waste orifice like a reptile. Also like a reptile it has venom - specifically in its claw. Finally, and unusually for a mammal but normal for a reptile, it lays hard, waterproof eggs.

Amphibians themselves have limbless young that have gills (like fish) and swim in water. The adult breathes air through lungs and moist skin and has limbs to get around on land.

If we look at the skeletons of all the mammals, we find that they are composed of the same bones. The bones may be adapted differently and have different shapes but they are exactly the same bones connected to each other in the same order.

The diagram below shows the fore and hind limbs of a number of mammals. The main bone plan for these limbs is indicated in the centre of the diagram. Around that are the adapted structures used by the animals and what they use the limb for.

We can see clearly, the same bones are used in all cases. Note the single upper arm / thigh bone and the double fore arm / lower leg bones are present in all the examples. All have five digits except the four toed pig and single toed horse which have lost their other toes. This basic plan is also found in birds and reptiles.

Evolution works by adapting existing structures. The similarity of animals' bones structures is excellent evidence for evolution. If all animals were independently created one would expect different functionality to be expressed in different ways. Instead we find the same structures adapted to do different things.

Limbs

The natural and nested hierarchical classification of animals (and plants) plus their common structures are very strong evidence that evolution has occurred. It is not, however the only evidence.

The DNA Record

Dioxyribose Nucleic Acid (DNA) is a substance found in all living things on Earth. This is a chemical that is used in reproduction and carries a series of instructions called Genes. These genes regulate the creation of proteins and control the development of the young. The exact genetic sequence in a creature's DNA determines whether its young develop as a cat, banana, mushroom or human.

In recent years the genetic sequences of many species has been determined. When these are compared, it is found that species that are closely related have similar sequences of genes. More distantly related species have more differences in their genetic sequences. This is because genetic material naturally changes over time because of mutations. If two genes split from a common ancestor in the recent past there will be less differences between them as only a little time has elapsed. On the other hand, if the split occurred a long time in the past, there will have past enough time for many more differences to have built up.

The following table compares the DNA sequences of animals and plants to humans.

The first row indicates the difference among humans (less than 0.1%)

Species
Type
Percent of DNA
Similar to Humans
Humans Mammal - Hominid 99.9
Chimpanzee Mammal - Primate - Ape 96
Rhesus Monkey Mammal - Primate - Monkey 93
Cat Mammal - Carnivore 90
Cow Mammal - Bovine 80
Mouse Mammal - Rodent 75
Zebrafish Fish 70
Chicken Bird 60
Fruit Fly Insect 60
Banana Plant 50

Studies of DNA sequences also indicate relationships between animals that superficially look very dissimilar, for example between Whales and Hippos. We will see later that this relationship is also backed up by the fossil record.

The comparison of genes also yields a hierarchy of species. This hierarchy matches very closely the hierarchy derived by looking at form and features. The family tree derived from looking at form and features is the same family tree that appears when genes are compared. This implies that the family tree is real. If species were separately created, these relationships would not exist. The family tree is evidence of common descent and it is confirmed by studying form and features as well as by comparing the DNA record.

This hierarchical matching is explained by the Theory of Evolution. The changes to DNA are reflected in the changes to form. Creatures that are closely related have closely matching DNA.

Humans have many similar features to apes and share a lot of their DNA.

Humans even share genes that are no longer functioning with other primates.

All mammals have four genes that control the manufacture of Vitamin C. Primates are one of the few mammal orders that cannot manufacture their own Vitamin C. They have to obtain it from their diet, mainly from citrus fruit.

There are four genes that are involved in the manufacture of Vitamin C and each gene controls one of the chemical steps in the process. In primates one of these genes, the fourth, has mutated so it no longer works. A single nucleotide (one letter of the genetic code) is missing in the gene. The same nucleotide is missing in all primates.

Inactive or dead genes are called Pseudogenes.

The three working genes have no end product as the fourth and final stage in the process no longer happens. All four genes including the non-working pseudogene are common to primates and to humans.

The fourth gene has been rendered inoperative by a bad mutation in an ancestor primate about 40 million years ago. The three working genes and the pseudogene have been passed to all its descendants including humans. Because humans have inherited this gene, they are incapable of manufacturing Vitamin C. Humans, like apes and monkeys, obtain their required Vitamin C from citrus fruit in their diet. Lack of Vitamin C causes a disease called Scurvy.

Humans carry about 30,000 genes of which some 2,000 are pseudogenes. In other words over 6% of all human genes are inactive.

The presence of the same inoperative gene in a closely related set of animals is very strong evidence for Evolution. The presence of three working genes and a fourth that is inoperative is very difficult for Creation or Intelligent Design to explain. Why design humans with three genes that work but which have no end product as the forth in the set doesn't work?

There are another group of genes called Olfactory Receptor Genes (OR Genes).

In mice there are over 1500 OR Genes which are used for smell. Each gene produces a receptor for an odour or smell. Mice are very dependent on their sense of smell. Primates have only 800 OR Genes but only 400 of these are active. Primates tend to be out during the day so vision is more important to them than smell. Primates have 400 OR genes that are inactive (pseudogenes). Humans have these 400 pseudogenes inherited from ancestors whose sense of smell was more important. These dead OR genes in humans are similar to the dead OR genes possessed by primates.

In dolphins, 80% of their OR genes are inactive. These dead genes resemble those of land mammals. The presence of genes used for smell in an animal living its entire life in the water makes no sense unless dolphins evolved from land dwelling ancestors.

The similarity of pseudogenes between species is strong evidence for evolution. Why would different species carry dead genes unless they evolved from creatures that used those genes?

All life on Earth uses either DNA or a simpler molecule, RNA. The Genetic Code itself is made up of a sequence of four DNA bases (or letters). The same four letters are used in all organisms and generate the same amino acids regardless of whether the sequence is in a bacterium or a human. The exact sequence of amino acids (which differ in different organisms) produce all the different proteins and enzymes used by all life.

The fact that a piece of DNA in a bacterium codes for the same amino acid as in a human cell is strong evidence of common descent.

Endogenous Retroviruses (or Virogenes) are pieces of gene sequences left from ancient viral infections in an organism. They are always passed on to the next generation of the organism that received the infection. This fixes the virogene in the Chromosome (a collection of genes) in a specific portion of its genetic sequence. This is a rare event that happens at random.

Many Virogenes have been found in the same position of the Chromosomes of different species. This too suggests a common ancestry.

Adenosine triphosphate (ATP) is the chemical used to transport energy in all extant life. Again this is evidence of common descent.

All organisms that can see or detect light do so using a common set of light-sensing proteins called Opsins, again suggesting common descent.

The body plan of all vertebrates is controlled by the same family of genes, called the Homeobox family.

Many of the sugars and proteins used by all organisms have two mirror image forms. There is no advantage to using one or the other but all Earth life uses the same version. This is also evidence of a common descent for all life.

Life on Earth shares a common biochemistry (including the use of DNA / RNA for replication and protein production). All of these observations are best explained by the Theory of Evolution and the common descent of all life on this planet.

Developing Embryos

Embryology is the study of the development of animals. The study of embryos provides very powerful evidence of Evolution in animals.

All vertebrates begin development in the same way. They resemble embryonic fish. As they develop, they lose components, move vessels and organs and end up as very different animals.

Human and other mammalian embryos develop amphibian characteristics from their fish-like beginnings. They then take on forms shared by reptiles before developing mammalian characteristics.

The fish stage is characterised by structures called Branchial Arches, a series of grooves in the embryo. In fish these develop straight into the animal's jaw and its gills. For mammals these same arch structures eventually develop into a jaw, the bones of the inner ear, the larynx, tonsils, carotid artery and neck muscles.

Human Embryo
Human embryo at 32 days showing four branchial arches.

Similarly, blood vessels and nerves begin development by resembling those of fish before changing shape and direction and morphing into amphibian, reptilian and mammalian forms. For humans, the original six blood vessels in the fish stage become three.

Reptile embryos also begin development by resembling fish. They too develop into their reptilian forms via an amphibian stage. It is notable that embryos of reptiles never go through a mammalian stage during their development.

Amphibian embryos also begin development from a fish-like stage. They never pass through a reptilian or mammalian stage.

The embryos of fish convert the branchial arches straight into a jaw and gills.

Human embryos develop three sets of kidneys, discarding the first two which resemble the kidneys of jawless fish and reptiles.

The development of embryos is very strong evidence of Evolution.

Mammalian embryos do not begin by resembling a smaller version of the mammal. Instead they appear to go through a complete evolutionary cycle making convoluted changes as if their development program contains their entire evolutionary history. For all vertebrates, the developmental sequence of the embryo follows the sequence indicated by animal classification, DNA sequences and (as we shall see next) the fossil record: fish, amphibian, reptile, mammal.

With genetic changes it is always easier to add a new program to existing code than to re-design everything from the beginning. When land dwelling animals developed lungs, the genetic program for gills remained in place so the embryo begins by developing gill-like structures. The genes for producing lungs are additions to the existing genetic code. These are triggered after the gill-producing genes. The embryo then goes on to develop lung-like structures.

Similarly, human embryos develop a tail which is later re-absorbed.

The development of embryos is strong evidence for Evolution.

It is noteworthy that mammalian embryos develop into a foetus by following the same evolutionary sequence that we have already encountered elsewhere. That sequence of fish to amphibian to reptile to mammal keeps appearing as if it is trying to tell us something.

The Creation Hypothesis has no explanation for the sequence of embryonic development. The convoluted pathway of the embryo (especially the building and abandoning of structures like kidneys) is not evidence of any intelligence in the design.

Reptiles have three bones in their lower jaw and one in the ear. In mammals, two of the lower jaw bones have been co-opted to make three bones in the ear, leaving one for the lower jaw.

The embryo of the pygmy oppossum, a marsupial mammal, goes through the same development after it has been born and while it is in its mother's pouch. It starts off with three bones in its lower jaw. These slowly shrink and move back until they join the single bone in the ear to end up with the standard mammalian system of three ear bones.

[Introduction]   [Fossils and their Secrets]


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External Evolution Links

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Vertebrates
A brief introduction to the Vertebrates.

DNA
Introduction to DNA, the replicator molecule.

Embryology
The development of embryos.