Many lizards have a so-called ‘third eye’, more formerly known as a parietal or pineal eye, which is located smack dab in the middle of their heads.
If you dissect a parietal eye, you’ll see that it very much resembles a normal eye, with structures similar to a cornea, lens and retina, as well as a nerve projecting from the light-sensitive retinal cells.
Just like our normal (‘lateral’) eyes, these structures absorb light and translate it into electrical signals, which are then sent to the brain, communicating information about the abundance and composition of light in the environment. Though the function of the parietal eye is not fully agreed upon, it appears that it at least helps lizards to know how long they need to stay in the sun to warm up, since removing it or blocking it from sunlight leads to lizards staying out the sun longer than normal.
While this third eye is only found in lizards and the closely-related tuatara, there is evidence in the fossil record that it was formerly much more widespread. If you look at the skulls of many types of fossil reptiles, you’ll find a little hole at the top of their skulls, just like in modern day lizards that have a parietal eye. What’s also interesting is that some fossil species that show similarities to birds, crocodylians and turtles also have this hole in their skulls, despite the fact that these modern birds, crocs and turtles do not have a parietal eye.
For example, the image above is a phylogenetic hypothesis showing a sequence of early reptiles that all have a hole at the top of their skulls (parietal foramen) until the appearance of some of the earliest turtles (Proganochelys).
Recent research has isolated a couple of proteins that are expressed in the parietal eyes of lizards. These proteins, parietopsin and parapinopsin, function as pigments that absorb light in the parietal eye .
In a recent study , I found both the parapinopsin and parietopsin genes in birds, crocodylians and turtles, but they are full of mutations that prevent the formation of functional proteins. This is consistent with the idea that the ancestors of birds, crocodylians and turtles had parietal eyes with functional parietopsin and parapinopsin, but ultimately lost the need for them. The reasons for the loss of this organ are a bit mysterious, but the consistent story told by both genetics and the fossil record makes a convincing argument for these birds, crocs and turtles having evolved from animals with a third eye.
Questions for Creationists
Why did the Creator create birds, crocodylians, and turtles with remnants of genes that are found in the ‘third eyes’ of lizards? Is it just a coincidence that fossils of animals that look similar to these species had holes in their skulls that correspond with the parietal eye of lizards?
As I discussed in the previous post, the fossil record tells a story that at first seems implausible: birds are descendants of dinosaurs. Part of what’s surprising about this idea is that dinosaurs typically appeared very reptilian, whereas birds do not.
Without providing a formal definition of “reptile”, you probably have a general image in your head. This is because reptiles possess a suite of characteristics that intuitively unite them into a group. For instance, reptiles are covered in scales, walk around on all fours, have tails, typically have simple conical teeth and warm up by basking in the sun.
Birds, by contrast, are covered in feathers, walk around on just their hind legs and/or fly, lack tails, have no teeth whatsoever, and are able to generate their own heat, similar to mammals.
Anybody that is at least vaguely aware of animal diversity probably would never mistake a bird for a reptile. So besides a pattern in the fossil record and remnants of tooth genes in their genomes, is there any other evidence that birds are descended from dinosaurs and, ultimately, other reptiles?
One line of evidence comes from comparisons of DNA. When researchers have compared the genes of birds, reptiles, and other animals, they find something that perfectly fits the conclusion of the fossil record: birds are genetically nested within reptiles. In fact, crocodilians are more genetically similar to birds than they are are to turtles or lizards. As just one example of a study that demonstrates this, Chiari et al.  compared 248 genes, with a total of 187,026 letters of DNA, among multiple species of reptiles, birds and other vertebrates and found this very pattern:
The green branches on this phylogenetic tree indicate lizards, red are turtles, blue are crocodilians and purple are birds.
The link between crocs and birds isn’t entirely surprising to anatomists, who have long remarked that modern and ancient crocodilians share a number of traits with dinosaurs, including teeth set in sockets (thecodonty), holes in the skull in front of the eyes and in the lower jaw (antorbital and mandibular fenestrae), and an extra ridge (trochanter) on the femur. However, birds no longer have most of these traits, and the one trait that they do have (antorbital fenestrae) is not found in modern crocodilians. As such, this conclusion was not always intuitively obvious.
Nonetheless, here we have an excellent example of where DNA and fossils tell the same story. Fossils appear to document a transition from large reptilian progenitors to modern birds and DNA suggests that birds are not only relatives of reptiles, but are descendants of reptilian ancestors shared with crocodilians, turtles and lizards..
Questions for Creationists
Why do birds have DNA more similar to crocodilians than crocodilians do to turtles and lizards? Is it just a coincidence that bird DNA and the fossil record seem to be telling the same story, that birds are descended from reptiles? What kinds of evidence might overturn this hypothesis?
Everyone knows that dinosaurs are extinct. As children, many of us gazed in awe at the fossils of these magnificent beasts. As adults, a lot of us still do!
Except that dinosaurs aren’t extinct, at least based on the most recent interpretations of the fossil record and analyses of DNA. The collective evidence points to a conclusion that once seemed improbable: birds are dinosaurs. I still recall the awe and wonder that beheld me when I learned this in college, and when I’ve taught it to children (all of whom are bonafide dinosaurs experts), I can see the same amazement on their faces.
So what evidence is there in the fossil record for this supposed ancestor – descendant relationship?
Prior to the Triassic, there were a lot of reptilian looking animals that no longer exist today. One such animal, Protorosaurus, has been found in rocks dating to about 260-251 million years ago (Ma). Typical of its contemporaries, it walked around on four limbs, each of which terminated in five fingers or five toes, possessed a long tail and teeth, and was almost certainly covered in scales. At this point in time, Protorosaurus and its fellow reptiles had seemingly little in common with today’s birds.
Not too much later, about 245 million years ago, animals like Asilisaurus appear in the fossil record. Though this species likely walked on all fours, it had shorter arms, suggestive of an increased ability to walk and/or stand on its hindlimbs.
In another nine million years, we see animals like Marasuchus (236-234 Ma): clearly reptilian in form, very dinosaur like, and notably bipedal, just like birds.
Eodromaeus and its kin are among the earliest true dinosaurs, popping up a mere five million years after Marasuchus (231.4-229 Ma). One of its typical dinosaurian traits is a hip socket with a hole in it (perforate acetabulum). What’s additionally notable about this species and some of its contemporaries is how its fingers have changed. Modern birds do not have fingers, but their wing bones terminate in what appears to be the remnants of three fingers. Starting this trend toward digit reduction, Eodromaeus has five fingers, but the ring and pinky are very reduced in size.
Eodromaeus hand, showing the reduced ring finger (IV) and pinky (V)
Fast forward about 30 million years, and we have more modern-looking dinosaurs on the scene. Coelophysis (203-196 Ma) is typical of the early carnivorous dinosaurs (theropods), and continues the march towards birdiness. The pinky finger is practically non-existent at this point, and the toes have also reduced in number. Whereas earlier dinosaurs and other reptiles have five toes, Coelophysis has only four, with a tiny remnant of the fifth high up on the foot. Notably, birds have four toes, three in the front and one in the back, so this trait had already appeared at least 200 million years ago.
Foot (left), hand (right)
Whereas Coelophysis had four fingers on its hands, Sinosaurus (201-196 Ma), appearing two million years later, only has three fingers, having lost the ring finger altogether.
While other bird-like traits accumulated over time, perhaps the most significant change is found in rocks that date to 50 million years after dinosaurs like Sinosaurus. Archaeopteryx (150.8-148.5 Ma), the first documented transitional fossil, has a striking mix of bird- and reptile-like traits. Perhaps most significantly is the appearance of feathers in this species.
There is reason to think that feathers appeared prior to Archaeopteryx, however. Soft tissues like feathers don’t typically preserve well as fossils, but over the last 20+ years, a number of exceptionally preserved specimens have demonstrated that plenty of non-flying dinosaurs had feathers. This suggests that these structures didn’t appear for the purpose of flight, but rather for a simpler function, such as thermoregulation. Just like hair keeps us and other mammals warm, feathers provide a similar insulating layer for birds.
Archaeopteryx clearly had wings, though, suggesting some ability to glide or perform flapping flight. It had another bird-like feature, known as the furcula. Also known as the wishbone, the bone frequently broken apart as a Thanksgiving dinner ritual in the United States, this bone formed by the fusion of the two clavicle bones present in earlier species like Coelophysis. This fusion is thought to be important in withstanding the stressors caused by flight, but it is also present in many other carnivorous dinosaurs, suggesting it initially appeared for a different reason.
Despite these innovations, Archaeopteryx is still not as bird-like as you’d think. For one, it still very clearly had three fingers, along with claws, on its hand. It also had a long bony tail, a structure reduced to a nub (pygostyle) in modern birds. Last but not least, Archaeopteryx had teeth, whereas birds have lost their teeth entirely in favor of a beak made of a protein called keratin.
After another 15 million years, other dinosaurs, like Sinornis (135 Ma), were just a few steps away from modern birds. The tail bones had finally become shortened and fused into a pygostyle in Sinornis, providing a structure tail-feather attachment. The sternum also became keeled increasingly keeled, allowing for the attachment of more powerful flight muscles, suggesting that Sinornis was a better flyer than Archaeopteryx. Despite these innovations, Sinornis still retained teeth and three distinct clawed fingers, traits that are not present in modern birds.
40 million years later, when tyrannosaurs and pachycephalosaurs were still roaming the earth, some extremely bird-like animals appear in the fossil record. At first glance, Ichthyornis (93-83.5 Ma) may be difficult to discern from a modern seabird. Many of the limb bones, including the fingers have become fused in Ichthyornis, resulting in a skeleton that was probably well-adapted for powered flight. Nonetheless, as one of the final holdouts of its reptilian past, Ichthyornis still had teeth. Interestingly, however, its jaw tip appears to be covered by an incipient beak, suggesting the transformation is nearly complete.
After most dinosaurs disappeared from the fossil record, coinciding with geological evidence for a disastrous meteor impact and intense volcanism, birds persisted and began to really thrive. Among the earliest species is Waimanu (60 Ma), which appeared just five million years after this mass extinction event. Not only does Waimanu have the appearance of a modern bird, paleontologists think it was the earliest known penguin, suggesting the surviving bird species have already begun to resemble some of their modern forms.
Over a period of about 200 million years, the fossil record appears to document the gradual appearance birds from reptilian forebears. With the advent of bipedalism, the reduction in fingers and toes, derivation of feathers and wings, reduction of the tail, and loss of teeth, fossils seem tell the story that birds are, in fact, dinosaurs. Do not hesitate to remember this the next time you feed a duck or eat a chicken wing!
Question for Creationists
Where did all of these fossil animals go? Could they not fit on Noah’s ark? Wouldn’t species with some capacity for flight, such as Sinornis, Archaeopteryx, and Yi qi, be able to avoid the Flood? Why does the fossil record appear to document a transition between reptilian animals and birds? If Noah’s Flood is responsible for the placement of these fossils, why did they appear in this particular sequence? Is it just a coincidence that the fossil record appears to document birds descending from ancestors with teeth and birds have remnants of tooth genes in their genomes?
The molecular basis for taste is relatively straightforward. On your tongue, you have numerous taste buds that harbor cells with little proteins hanging out on the top. These proteins have the capacity to bind a number molecules on your tongue, and thereby transmit information regarding nutritional content.
One of these proteins is TAS1R2, which, along with the protein TAS1R3, binds sweet tasting molecules. This sweet receptor is what allows you to savor the delicious sucrose (table sugar), fructose (fruit sugar) and even artificial sweeteners such as saccharin and aspartame. If you love cake, ice cream, and cookies, be grateful that you have a functional sweet receptor!
Not all animals are fortunate enough to enjoy these treats, however, and evolution is likely to be blamed. Many species are particularly adapted to eating foods that are nearly devoid of sugars, and therefore are not expected to benefit from maintenance of the gene encoding TAS1R2. Indeed, scientists  have found that a number of carnivorous mammals, including cats, hyenas, seals, the banded linsang, fossa and Asian small-clawed otter have a pseudogenized (nonfunctional) version of the TAS1R2 gene.
Asian small-clawed otter
This helps explain why cats behaviorally seem uninterested in sugar. The scientists also confirmed that the Asian small-clawed otter also is not drawn to sweets, consistent with its TAS1R2 pseudogene. By contrast, they found that the spectacled bear, which has an intact TAS1R2 gene and is a known devourer of sweet things like fruits and honey, prefers sugary solutions over water.
These data suggest that the ancestral carnivores did eat sweets on occasion, but certain species avoided sugary foods for so long that sweet receptors were no longer necessary. Eventually mutations rendered the TAS1R2 gene nonfunctional in different carnivore lineages, rendering these species impervious to the effects of sweets.
Questions for Creationists
Why did God create some carnivores with a nonfunctional version of the sweet taste receptor gene? Would it not have made more sense for Him to create them without the gene altogether? Is it just a coincidence that He also created other animals with specialized feeding strategies, such as giant pandas and whales, to lack certain taste receptors?
Perhaps you haven’t thought of it much before, but relatively few species of insects completely lack wings. One kind of wingless insect is known as a silverfish, an animal that perhaps you have discovered crawling in your home or hanging out in your pantry.
Typical of insects, they possess six legs, a chitinous exoskeleton, compound eyes and a pair of antennae. Unlike most other insects, they are wingless and have three filaments that jut out from the tail portion of their bodies. The latter traits are typical of multiple species of insects beyond silverfish, including the firebrat and bristletails, a group that I was taught was called Thysanura growing up.
Despite thysanurans seemingly being united by these distinctive characteristics, when scientists began comparing insect DNA, they found that thysanurans didn’t group together. Instead, the results from DNA suggest that they represent two distinct lineages of insects that just happen to look very similar. Below is a molecular phylogeny that included 1478 genes from 144 species of insects and insect-like animals (arthropods) :
You can see the thysanuran species at the top of the phylogeny. One lineage of thysanurans is now called Archaeognatha, which includes the animals below:
The next group is called Zygentoma, which includes the silverfish and others, such as some oddball species that are blind, lack color and live exclusively with ants and termites:
Despite their striking similarities to one another, zygentomans are actually more genetically similar to winged insects, with forms as diverse as praying mantises, butterflies and beetles. This might seem surprising, but it’s quite plausible if evolution is true.
One scenario in which this is possible is if Archaeognatha and Zygentoma independently evolved a very similar body form, known as convergent evolution. Evolutionary biologists typically expect this to occur when different organisms adapt to very similar lifestyles. However, since these lineages split off in relatively rapid succession, it’s more likely that the earliest insects looked like thysanurans, and archaeognathans and zygentomans retained this ancestral body type.
Questions for Creationists
If God created archaeognathans and zygentomans, as well as the DNA that determines how they look, why is it that their DNA is so different? Shouldn’t animals that look similar have more similar DNA?
Below is a picture of an Atlantic spotted dolphin (Stenella frontalis), which very clearly has forelimbs (flippers) but no hindlimbs, typical of whales.
But when this and related species are still embryos, you can see that tiny hindlimb buds form .
If you look at a series of embryos through their development, the hindlimb buds form but then they disappear.
Interestingly, dolphins seem to retain some of the genetic developmental machinery to make hindlimbs. Occasionally, people have found individual dolphins that have hind flippers, such as the one in the picture below.
This is called an atavism, and is thought to arise from one or more mutations that somehow turn the development of the hindlimbs back on.
Together, this is a remarkable example where DNA, fossils and ontogeny all tell the same story, specifically that whales descended from ancestors that walked on four legs. These animals appear to have gradually lost their hindlimbs, presumably as an adaptation to streamline their bodies for swimming, but their ontogeny seems to retain a record of their fully-limbed past.
Marsupials are a group of mammals generally characterized by having their young develop in a pouch, known as a marsupium. Besides this trait, there isn’t anything obvious about them that screams out that they are more closely related to each other than they are to other mammals. When you place a kangaroo, Tasmanian devil, koala, marsupial mole, antechinus, bilby and cuscus side-by-side, they probably don’t strike you as cousins.
And yet, when we look at their DNA, we find that they are more genetically similar to each other than they are to other mammals. Below is a phylogeny  estimated from thousands of letters of DNA, and you can see that the marsupials (at the top in purple) cluster together to the exclusion of all other mammals.
What’s particularly interesting about their genetic similarity, is that where they live also seems to point to a common ancestry. Some marsupials, namely shrew opossums, opossums, and the monito del monte, live in South America and, in the case of the Virginia opossum, North America as well. The rest of the marsupials all live in Australia and the surrounding islands. Below is a world map showing the distribution of modern day marsupials.
What adds to this interesting pattern is that when you look at the marsupial phylogeny above, the American marsupial lineages (Caenolestidae, Didelphidae+Caluromyidae, Microbiotheriidae) split off one by one. All of the remaining marsupials, which are clustered together, hail from Australasia. To state this in no uncertain terms: Australasian marsupials are more genetically similar to each other than they are to American marsupials.
So here we have an example where both biogeography and DNA tell the same story: a single marsupial ancestor colonized Australasia and then split into many different species with a multitude of distinct body forms, ranging from kangaroos to marsupial moles and koalas to cuscuses.
Questions for Creationists
Why do marsupials, despite looking so different from each other, have such similar DNA? If God created the DNA ‘blueprint’ for all life, and DNA makes bodies look the way they do, shouldn’t marsupial moles have DNA more like other moles, and Tasmanian devils have DNA more like other carnivorous mammals? Why do most marsupials live in and around Australia? Is it just a coincidence that all Australasian marsupials are more genetically similar to one another than they are to American marsupials? If they didn’t evolve from a common ancestor, did they all walk together from Noah’s ark to Australia? If people brought them to Australia, why did they mostly only bring marsupials?
Crocodilians, which include crocodiles, gharials, caimans and alligators, are represented by relatively few species today. Not only are these animals not particularly speciose, they are also quite similar in appearance and habit. Looking at them, they are unmistakably crocodile-esque, with their toothy smiles and elongate bodies embedded with rows of bony scales. Crocodilians are generally ambush predators that hunt in the water or at the water’s edge. While some species mostly hunt fishes, the stereotypical image of crocodilians lying in wait for an unwitting animal to take a drink is not uncommon. Though they seem quite comfortable in water, crocodilians have a sprawling, somewhat awkward posture on land. Nonetheless, they will frequently leave the water to rest and bask in the sun.
Once upon a time, there was quite an impressive diversity in the forms of crocodilian-like animals, many of which appear to have had very different lifestyles from modern species. One group of these animals was the thalattosuchians, which were particularly specialized for living in the ocean. Some thalattosuchians superficially looked quite similar to modern crocodilians, particularly teleosaurids, which includes Platysuchus and Steneosaurus.
Others were more obviously adapted for an oceanic lifestyle, and would have looked quite different from your typical crocodile or alligator. These species include Geosaurus, Rhacheosaurus and Dakosaurus, known collectively as metriorhynchids. If you look closely at Geosaurus, you can see that the limbs were more fin-like in shape, and both Geosaurus and Rhacheosaurus preserve outlines of a tail fin, demonstrating evidence of their strong swimming abilities.
Thalattosuchians appear in rocks estimated to be 199.3 million years old, and then seemingly disappeared 93.9 million years old . Despite this long and successful history, for better or worse, they can no longer be found in our seas.
Questions for Creationists
Where did the thalattosuchians go? Why would God create them only to have them completely disappear? Since they lived in oceans, shouldn’t they have survived Noah’s flood? Why do modern crocodilians have very similar lifestyles whereas the other crocodilians seemed to have lived very differently?
Manatees and the dugong, known collectively as sirenians, are herbivorous, aquatic mammals that are generally restricted to shallow, tropical waters. Like whales, sirenians have reduced the amount of hair on their bodies, have forelimbs shaped into flippers, lack external hindlimbs and have a paddle-like tail.
Despite their overall similarities, the DNA of sirenians is much more similar to that of elephants and the DNA of whales is much more similar to hoofed mammals like cows and giraffes. This suggests that both sirenians and whales independently adapted to living in an aquatic medium. In fact, the fossil record of whales suggests a transition from a land-based habitat to a completely aquatic way of life. Do sirenians show the same pattern?
Indeed they do! One of the earliest sirenian species appearing in the fossil record is Pezosiren, a mammal with an unmistakably sirenian-like skull, but the rest of its skeleton clearly suggests that it had the ability to walk on land. Unlike modern sirenians, this animal had forelimbs that are not shaped like flippers but instead were used to support their weight on land, as well as hindlimbs and a distinct hip bone (pelvis). Pezosiren has been found in rocks estimated to be ~47.8 million years in age, similar to the age that walking ‘whales’ were also found roaming the earth.
More recent sirenian fossils show evidence of fully committing to an aquatic lifestyle, including Halitherium, which is found in rocks estimated to be ~38 million years old. This species and similarly dated fossils had modified their forelimbs into flippers, possessed thick and dense ribs to provide ballast, and reduced their hindlimbs, presumably to minimize drag. Though it looked very much like modern manatees (see below) and dugongs, it had a better-developed, albeit very reduced, pelvis+hindlimb complex.
In addition to their better-developed limbs, early species of sirenians had a number of other traits that manatees and the dugong have lost. Pezosiren and others had multiple vertebrae in the hip region (sacral), much like their land-dwelling elephant relatives, whereas most fossil and all modern sirenians have fused these into a single bone. Modern sirenians also have reduced their teeth to a great extent compared to their fossil forebears. Earlier species had permanent premolars, canines and incisors, whereas modern species lack these teeth (dugongs have only one incisor). See below for a diagram of a fossil sirenian (Protosiren, ~47.8 million years old) showing the positions of the premolars (P), canine (C) and incisors (I).
Questions for Creationists
Where did the dozens of other sirenian species go? Given their aquatic adaptations, wouldn’t they have survived Noah’s flood? Is it just a coincidence that molecular phylogenetics shows sirenians as being genetically similar to land mammals like elephants and there are sirenian fossils that appear to document a transition from land to water? Is it coincidence that we see parallel evidence of a land to water transition in whales?
When children learn about different animals and how to classify them, they are often taught that three features unite mammals: hair, milk, and live birth. This last trait is likely taught to contrast mammals with the many other vertebrates that lay eggs.
But this last point is not correct. Nearly all mammals give birth to live young, but a handful do lay eggs. These are known as the monotremes, which encompass the platypus and several species of echidnas or spiny anteaters, all of which live in Australia, Tasmania and New Guinea.
Echidna egg hatching
The fact that a few mammals lay eggs, plus that most other land-dwelling vertebrates do as well, points to the idea that the rest of mammals descended from egg-layers. So how might one test this hypothesis? David Brawand and his colleagues  had the idea of looking at the genomes of mammals to see if they have any remnants of egg yolk genes.
Besides monotremes, the remaining mammals can be divided into two general groups: (1) marsupials, whose offspring are born early in development and then finish developing in a pouch (marsupium), and (2) placental mammals, which develop with the help of a placenta connecting the mother to the fetus. When Brawand and his colleagues looked at the genomes of three placental mammals (human, dog, armadillo), they found remnants of two egg-yolk genes (VIT1, VIT3), both of which possessed loss-of-function mutations. These mammals share some loss-of-function mutations in the genes, suggesting that the genes were inactivated in a common ancestor. Similarly, the researchers found remnants of three egg-yolk genes (VIT1, VIT2, VIT3) in the marsupials they studied (opossum, wallabies), with shared loss-of-function mutations in each (Figure 1), which, again, imply loss in a common ancestor.
Figure 1. DNA sequence alignment of egg-yolk genes . Highlighted portions indicate loss-of-function mutations. Gallus gallus = chicken; Monodelphis domestica = opossum; Macropus eugenii and Wallabia bicolor = wallabies.
By contrast, at least one egg yolk gene is intact in the egg-laying platypus. Together, these data suggest that the inactivation of egg yolk genes in placental and marsupial mammals is connected with the loss of their egg-laying ability through evolutionary time.
Questions for Creationists
Why do mammals that do not lay eggs have non-functional egg yolk genes in their genomes? If these species do not lay eggs and didn’t evolve from ancestors that lay eggs, why would God have put these in their genomes? Why do some mammals share some identical loss-of-function mutations in their egg yolk genes genes?