A Primer on Evolution pt 2: Evidence

In part two, I will give a brief overview of the evidence for the theory of evolution. This is not an exhaustive compendium of all the evidence in support of the theory of evolution. It is already a long post, so I keep all my descriptions brief. If you are interested in learning more, I provide plenty of links to websites and peer reviewed papers all throughout.

It’s not absolutely necessary, but it may make more sense why this evidence is convincing if you understand how evolution works. For that, I suggest checking out part 1 of this primer first.

If you’re interested in how evolution relates to religion and whether it gives us any reason not to believe in God, check out this post. The current discussion will not touch on the subject, sticking strictly to the science.

The theory of evolution by natural selection is one of the most robust theories in science. Mountains of mutually corroborating evidence all points to the theory of evolution as the engine generating the diversity of life. It shows that all known organisms on earth are descended from a common ancestor. Some organisms split off on their own evolutionary path longer ago than others. The longer it has been since there was a common ancestor between two species, the less related those species are.


The Fossil Record:

The fossil record is one of the most referenced sources of evidence for evolution. It’s through radiometric dating of fossils that scientists can determine when the organism lived. Transformations of fossilized skeletons through time show the evolutionary path leading from one species to the next.

The fossil record is what tells the actual story of evolution. It’s through the fossil record that we can get a glimpse of what actually happened eons ago. Unfortunately, the fossil record is fraught with “holes” (that skeptics are often quick to point out as evidence against evolution). But, we are actually lucky to have any fossils at all.

Not all organisms that have ever died left fossils. In fact, only organisms that die and leave their remains in very special conditions will leave fossils behind for paleontologists to dig up. The following video illustrates what those conditions are.

Radiometric dating is used to determine where in the timeline of evolutionary history an organism belongs. For organisms that died in the relatively recent past, scientists used carbon dating to determine how old they are. Carbon-14 has a half=life of 5,730 years, making it effective only for fossils under 50,000 years old. This is very short in evolutionary and geological time scales. The following video shows how carbon-14 dating is done.

In order to date older fossils, scientists often used Uranium-Lead or Potassium-Argon dating. This can’t be done directly with the fossils, which contain little if any of these elements, but it can be done on the rock which the fossils are buried in.

Potassium-Argon has a half-life of 1.3 billion years. The uranium series from 238U to 206Pb, has a half-life of 4.47 billion years and the actinium series from 235U to 207Pb, has a half-life of 710 million years.

The fossil record is what allows us to build a phylogenetic tree which shows the ‘story’ of how a lineage evolved.

Also, when fossils are uncovered we can compare their anatomy and observe the geological paths that the organisms took as they evolved, which leads to the next two points: anatomical homology and biogeography.

Anatomical homology:

The basic idea of this is that organisms that appear vastly different often have surprisingly similar structures. Evolution builds off from already existing features, so it is much more parsimonious to maintain the anatomical makeup of past ancestors. This suggests that different species share a common ancestor.

Evidence - Anatomical Homology

Mammalian skeletons are shaped different, but they share structural homology.

This comparative anatomy can also be used to compare lineages through time. For instance, in whale anatomy, the changes in bone morphology of pakicetidae can be followed along it’s phylogenic tree to the modern whales and dolphins.


Evolutionary history of the whale: they began as land mammals.

Intermediate morphologies can be observed. For instance, the stapes, incus, and malleus of the mammalian ear are homologous to parts of the fish jaw and gill arches. The changes in this morphology can be traced through the fossil record of reptiles and early mammals:

Having three ossicles in the middle ear is one of the defining features of mammals. All reptiles and birds have only one middle ear ossicle, the stapes or columella. How these two additional ossicles came to reside and function in the middle ear of mammals has been studied for the last 200 years and represents one of the classic example of how structures can change during evolution to function in new and novel ways. From fossil data,comparative anatomy and developmental biology it is now clear that the two new bones in the mammalian middle ear, the malleus and incus, are homologous to the quadrate and articular, which form the articulation for the upper and lower jaws in non-mammalian jawed vertebrates. The incorporation of the primary jaw joint into the mammalian middle ear was only possible due to the evolution of a new way to articulate the upper and lower jaws, with the formation of the dentary-squamosal joint, or TMJ in humans. The evolution of the three-ossicle ear in mammals is thus intricately connected with the evolution of a novel jaw joint, the two structures evolving together to create the distinctive mammalian skull.



The distribution of organisms on earth corresponds, in part, to the relationship implied by biological classification. For instance, trilobites during the cambrian period were unable to swim the vast distances of oceans, yet can be found in both North America and Europe:

biogeography of north sea

This shows that, during this period, the continents drifted together to form a supercontinent (see figure below), closing the lapetus suture, and allowed the trilobite species to cross over. After the supercontinent split, the species became geographically isolated and both took different evolutionary paths – this phylogeny is supported by the fossil record (this phenomenon is actually used as evidence for the theory of continental drift).


Gondwana: supercontinent that existed from the Neoproterozoic (about 550 million years ago) until the Jurassic (about 180 million years ago).

The same phenomenon is also seen in shorter timescales on islands (with the Galapagos islands being the famous ones that Darwin explored). When organisms become geographically isolated, their evolutionary path can be observed in the fossil record, but also in more recent observations, like the recent findings of killer whales occupying different niches.

Vestigial Organs:

Evolution is not perfect. There is no engineer who can switch parts in and out in order to build organisms. Evolution must build upon what’s already there, making nested hierarchies, and this often leaves vestigial organs (along with vestigial genes). For instance, the recurrent laryngeal nerve:

This video contains a relatively graphic dissection of a giraffe, so squeamish people should beware.

Some fish have vestigial lungs, such as anabantoidei, snakeheads, and Lungfish. There are also vestigial legs in snakes, whales, and dolphins:

Human’s display a lot of vestigiality. Aside from the well known organs, such as the appendix, coccyx, goosebumps and wisdom teeth, we also retain non-functional ear muscles that other organisms (including some monkeys) can use to move their ears, as well as what’s known as Darwin’s tubercle, which is only found in 10% of the population. Humans still retain the plica semilunaris of conjunctiva, which is vestigial of the nictitating membrane.

The Occipitalis Minor is a muscle in the back of the head which normally joins to the auricular muscles of the ear. This muscle has varying trends of presence in different races of humans. The Palmaris longus muscle is a seemingly functionless muscle that’s absent in some people. The pyramidalis muscle is a muscle in the torso that is absent in 20% of the population, and doesn’t seem to have any adverse effects to those missing it. The same goes for the plantaris muscle.


An atavism is when a trait that has been lost due to evolution reappears because the genetic material for the train remains dormant. Dormancy can occur when the gene is deactivated, no longer expressed, or if some other gene that negates the gene becomes dominant. Atavism is observed, for instance, when some human children are both with tails.

humans born with tails atavism

Tail formation is partly controlled by the Wnt-3a gene, which humans possess.

In order to understand this error, it’s first important to note that all humans briefly possess tails while in the uterus. Specifically, during normal development, certain fetal cells develop into a tail and then regress as a result of programmed cell death, or apoptosis. Investigators have identified a gene called Wnt-3a as a principal regulator of this process, at least in mice (Takada et al., 1994). Researchers have also discovered that humans indeed have an intact Wnt-3a gene, as well as other genes that have been shown to be involved in tail formation. Through gene regulation, we use these genes at different places and different times during development than those organisms that normally have tails at birth. Should this process of gene regulation somehow go wrong, however, the likelihood (albeit rare) exists that a person could indeed be born with a true tail.


Parasite Coevolution:

As an organism evolves, so do its parasites.

Parasites like lice are completely dependent on the biology of its host. As a result, when the host evolves, the parasites also must evolve in order to survive. This is seen in the lice that infect great apes.

This isn’t seen only in parasitic relationships. Symbiotic relationships also lead to coevolution. This is called phylosymbiosis.


[D]ifferences in gut microbiome composition among non-human primates mirrors host phylogenetic relationships, a pattern known as phylosymbiosis, and this signal of host phylogeny persists across a range of timescales, regardless of diet.



We demonstrate three key findings. First, intraspecific microbiota variation is consistently less than interspecific microbiota variation, and microbiota-based models predict host species origin with high accuracy across the dataset. Interestingly, the age of host clade divergence positively associates with the degree of microbial community distinguishability between species within the host clades, spanning recent host speciation events (~1 million y ago) to more distantly related host genera (~108 million y ago). Second, topological congruence analyses of each group’s complete phylogeny and microbiota dendrogram reveal significant degrees of phylosymbiosis, irrespective of host clade age or taxonomy. Third, consistent with selection on host–microbiota interactions driving phylosymbiosis, there are survival and performance reductions when interspecific microbiota transplants are conducted between closely related and divergent host species pairs. Overall , these findings indicate that the composition and functional effects of an animal’s microbial community can be closely allied with host evolution, even across wide-ranging timescales and diverse animal systems reared under controlled conditions.


Comparative Embryology:

Just like with structural homology, comparative embryology looks at similarities in structure and development. All vertebrates have similar embryos that follow a similar developmental path.


Vertebrates preserved their early developmental pathways from zygote to newborn.

Even in land mammals, such as humans, embryos still contain vestigial tails and gills.


Human and bird embryos have gills and tails that disappear during development. These features are a holdover from our marine ancestors.

One of the most celebrated cases of embryonic homology is that of the fish gill cartilage, the reptilian jaw, and the mammalian middle ear (reviewed in Gould 1990). First, the gill arches of jawless (agnathan) fishes became modified to form the jaw of the jawed fishes. In the jawless fishes, a series of gills opened behind the jawless mouth. When the gill slits became supported by cartilaginous elements, the first set of these gill supports surrounded the mouth to form the jaw. There is ample evidence that jaws are modified gill supports. First, both these sets of bones are made from neural crest cells. (Most other bones come from mesodermal tissue.) Second, both structures form from upper and lower bars that bend forward and are hinged in the middle. Third, the jaw musculature seems to be homologous to the original gill support musculature. Thus, the vertebrate jaw appears to be homologous to the gill arches of jawless fishes.

But the story does not end here. The upper portion of the second embryonic arch supporting the gill became the hyomandibular bone of jawed fishes. This element supports the skull and links the jaw to the cranium (Figure 1.14A). As vertebrates came up onto land, they had a new problem: how to hear in a medium as thin as air. The hyomandibular bone happens to be near the otic (ear) capsule, and bony material is excellent for transmitting sound. Thus, while still functioning as a cranial brace, the hyomandibular bone of the first amphibians also began functioning as a sound transducer (Clack 1989). As the terrestrial vertebrates altered their locomotion, jaw structure, and posture, the cranium became firmly attached to the rest of the skull and did not need the hyomandibular brace. The hyomandibular bone then seems to have become specialized into the stapes bone of the middle ear. What had been this bone’s secondary function became its primary function.


Genetic Evidence:

The first bit of evidence from genetics that all organisms evolved from a common ancestor is quite simple: all known organisms on earth use the same material and mechanisms.

All organisms use the same nucleotides to build the same type of molecule (DNA).


Thymine makes two hydrogen bonds to adenine; guanine makes three hydrogen bonds to cytosine. Only with these hydrogen bond pairs will the DNA maintain a regular structure (no bulges or indentations) which can be ‘sensed’ by DNA repair proteins processing along the DNA strand. Because the GC pairing has three hydrogen bonds compared to the two in the AT pair, the GC base pairing is stronger. This fact is important for a host of biological functions.

All organisms use the same genetic code.

genetic code table

Three bases, called a codon, indicate which amino acid will be added to a growing polypeptide. A gene consists of a long series of bases coding for a specific sequence of amino acids in a polypeptide (ignoring introns and exons for simplicity). Due to the 3:1 nature of bases:amino acids, the length of a gene in bases is always at least 3x longer than the polypeptide in amino acids. One thing to notice is that most of the amino acids contain redundancies. Also of note, the redundancies occur by altering the third base in the codon, which is the base that binds weakest to the tRNA during translation.

The central dogma is known as the central dogma because it is universal to all organisms.


DNA is transcribed into RNA which is then translated into a protein (a polypeptide made up of amino acids). Reverse transcription is used by some viruses called retroviruses that are composed on RNA rather than DNA and by telomerase in eukaryotes to maintain telomeres.

The processes and replication, transcription, and translation are conserved in all organisms across all three domains of life.


RNA polymerase transcribes an mRNA strand. The mRNA strand is then read by the ribosome by pairing the correct tRNA, containing the anti-codon, to the codon on the RNA. Through the ribosome’s catalytic activity, the amino acid bound to the tRNA is added to the polypeptide strand. This catalytic activity also causes the mRNA to move through the ribosome and the tRNA to be ejected, presenting the next codon for the next tRNA bound to its associated amino acid. This process is repeated over and over until the ribosome reaches a STOP codon on the mRNA. The result is a protein.

And all organisms use the same amino acids with the same chirality.


Molecular structures of amino acids grouped according to their chemical properties. Selenocysteine is not a universally used amino acid; there is no codon for selenocysteine, but is instead incorporated into proteins via translational recoding.

There are also genetic similarities between related species. The similarities decrease as relatedness decreases and vice versa. These similarities can be measured using multiple sequence alignments of a gene sequence. Alternatively, since gene sequence directly translates into protein sequence (and protein sequences do not have codon redundancies present in gene sequences) one can do an alignment using a protein’s single letter code.


From my own research, this is a multiple sequence alignment (MSA) for the C-terminus of the MED13 protein (last 257 amino acids in the polypeptide) which is predicted to form a 4-helix bundle. Made using Clustal Omega. Amino acids are shown using their single letter designation; dashes indicate where there is no corresponding part of the sequence. Below the sequences, a * means sequence identity and a : means sequence similarity (amino acids are not identical but have similar chemical properties). The table at the bottom shows the % identity (exact same amino acids in the corresponding sequence). Species that are similar (eg Human and Mouse) have almost identical sequences (96.85%). Moving further away, the % identity decreases. All of the organisms except yeast (Saccharomyces cerevisiae) are in the animal kingdom; yeast is a fungus. In the MSA it is easy to see that yeast sequence has many areas where it does not align with the animal sequences, which one would expect given that yeast is in a different kingdom and therefore less evolutionarily related. Drosophila is second least related to human, which is expected due to being in a different phylum. These alignments agree with other lines of evidence for species relatedness.

Mutation is the main source of novel variation. These differences come about through random mutations, which are then seized upon by natural selection when they confer fitness to an organisms offspring. The rate of mutation has been calculated and verified. Mutations conferring fitness to an organism has been seen in my own research.

Mutations can occur to new genetic material by replication errorectopic recombination of chromosomes, retrotransposon mediated sequence transduction, gene duplication, gene fusion/fission, tandem repeats, and  endogenous retroviruses.

Tandem repeats as a source of genetic variation is applicable to man’s best friend: the dog. Tandem repeats are when some genes contain repeating sequences of nucleotides adjacent to each other. Wolves (and all breeds of dogs) have a high frequency of these tandem repeats. The differentials in these tandem repeats accounts for the vast diversity within Canis lupus familiaris. For instance, size is influenced by a “single nucleotide polymorphism” in the IGF1 gene (1).

After all that I’ve studied in cellular and molecular biology, I honestly don’t understand how half of it would make any sense without evolution; something as simple as a small change in a certain allele for a receptor protein or enzyme can have large (beneficial, detrimental, or neutral) affects to an organism. HOX genes are ubiquitous among animals, with mutations causing drastic changes in body plans.

I already discussed gene duplication in part 1 of this evolution series, so I’ll merely quote it here to reiterate:

New genes come about in a few ways. One is through random mutation of the DNA sequence in a gene, which alters the functionality of the protein it codes for. This functionality might be a change in what other proteins or molecules it can bind or associate with; gains, losses, or changes in mechanisms of enzymatic action; changes in stability; changes in solubility; etc. Another is through gene duplication, which can allow one copy of the gene to remain and continue its function while the other copy alters and takes on new functionality. This is something I saw in my own research, which the recently duplicated MED12 and MED13 genes into MED12L and MED13L, which are already taking on new functions.

Mitochondrial DNA is another interesting bit of evidence. The mitochondria (and chloroplasts) is an organelle that came about through endosymbiosis, when a mutual relationship between early eukaryotes and the bacterial precursor of mitochondria became inseparable.


Illustration of eukaryotic evolution.

Evidence to support endosymbiotic theory:


The MADDR evidence for endosymbiosis.

Mitochondrial DNA is primarily inherited from the maternal line (none of the father’s mitochondria make it into the zygote upon fertilization). This has allowed for the study of the maternal haplogroup. (There is a similar phenomenon in males with the Y chromosome being inherited only from the father – the paternal haplogroup – but this can only be studied in males). Scientists can discern a person’s (or other animal’s) evolutionary past in their maternal line using these changes in mitochondrial DNA.

One bit of interesting genetic evidence for evolution is the ability to turn on genes in a chicken to make a dinosaur. They literally turn back the clock on evolution through manipulating genes that are already in an animal in a process called atavism activation.


The skull in the center is from a chicken with certain genes ‘turned on’ in order to make it develop like its dinosaur ancestors.

Chromosomal Evidence:

The fusion of chromosomes in humans as compared to chimps shows a picture of our evolutionary past – humans and chimps share a recent (in evolutionary time) common ancestor (1).


Humans have 46 chromosomes while chimpanzees have 48. Scientists discovered telomeric sequences in the middle of human chromosome 2 that point to an end-to-end fusion of chromosomes in human’s evolutionary past.


Centromeres are where spindle fibers connect to condensed chromosomes during mitosis. Human chromosome 2 has an inactive centromere leftover from a fusion event in their evolutionary past.

Irreversible Complexity:

Irreducible complexity” is a simple concept. According to [Michael] Behe, a system is irreducibly complex if its function is lost when a part is removed1. Behe believes that irreducibly complex systems cannot evolve by direct, gradual evolutionary mechanisms. However, standard genetic processes easily produce these structures. Nearly a century ago, these exact systems were predicted, described, and explained by the Nobel prize-winning geneticist H. J. Muller using evolutionary theory2. Thus, as explained below, so-called “irreducibly complex” structures are in fact evolvable and reducible. Behe gave irreducible complexity the wrong name.


Complexity is irreversible instead of irreducible through The Mullerian Two-Step: add a part, make it necessary. Here is an analogy (from Talk Origins):


Step #1, add a part: the top-stone.


Step #2, make it necessary: remove the middle stone.


We now have an irreducibly complex stone bridge. None of the three stones can be removed without destroying the bridge’s function.

This is often talked about with the evolution of the flagellum. However, the evolution of the flagellum actually illustrates the idea of irreversible complexity (over irreducible complexity) perfectly: it used proteins from the type III secretion injectisome as part of the flagellum complex. This also makes the flagellum an example of how evolution uses already existing structures and builds onto them rather than just making new things from whole cloth.



Artificial Evolution:

Bacteria have been experimentally ‘evolved‘ in the lab on many occasions. through what is called Adaptive Laboratory Evolution (ALE).


Bacteria have also evolved enzymes that can break down synthetic materials not produced in the wild, such as the plastic poly(ethylene terephthalate) (1)(2)(3), nylon, and various other plastics.

But human-caused evolution has been going on since before laboratories even existed in the form of pet, crop and livestock domestication.




Despite what some creationists say, the banana humans use as food definitely evolved, even if it was done on purpose by humans, as have many other fruits.

Evolution Observed in the Wild:

Speciation of Anolis lizards in the Caribbean.

Morphological changes in Stickleback fish show adaptation.


The lizard Podarcis sicula evolves a new organ (cecal valve).

A relatively simple mutation changed Ciona intestinalis simple single chambered heart into a more complex multichambered one.

2019-03-20 23_52_12-Window


The evidence in support of evolution by natural selection is overwhelming. There is no controversy about the theory. The word theory, in this case, is meant in the scientific, rather than colloquial, sense – a model supported by evidence, observation, and experiment. To anyone who doesn’t have ideologically driven motives, the evidence available should be convincing.

Further Reading

TalkOrigins is a great site with a compendium of evidence for evolution.

The Origin of Species by Charles Darwin (full book free online)

Wikipedia article on the evidence for evolution.

Answers to Common Creationist Arguments