10E God Created Crocodiles, Birds, and Fish (optional excursus)

An excursus is similar to an appendix and provides a digression from the main text. The excursuses are completely optional and are not part of the course. 

The Conclusion of the 5th Day.

Although God designed the DNA in the original vertebrate fish for the eventual development of vertebrates in land and sky, God might also have intervened in further genetic changes in tetrapods and birds up to nearly the end of the Mesozoic Era (100 Ma), when modern birds and crocodiles appeared in the fossil record, which was the conclusion of the 5th day: crocodiles and fish filled the seas (lakes and oceans), and birds walked on land. In addition to looking at the end of the 5th day, this chapter reviews the changes that took place as vertebrates adapted to the land and sky.

Genesis 1:22 “Be fruitful and multiply, and fill the waters in the seas, and let birds multiply on the earth.” There was evening and there was morning, a fifth day.

As with v. 20 (let the seas bring forth), but differing from v. 21 (God created), the term for birds in v. 22, op, includes both the birds and insects (flying creatures). There is probably an allusion in “let birds multiply on the earth” to the physiological and evolutionary connections between birds and dinosaurs and dominance of the dinosaurs on land. Paleontologists classify the dinosaurs as “those archosaurs closer to birds.”

Figure 10E-1 shows the progression of land animals in the fossil record of the Late Paleozoic and early Mesozoic (Figure 10E-2).  Amphibians appear in the fossil record in 340 Ma and reptiles shortly thereafter (320 Ma). There were two groups of reptiles, diapsids and synapsids. The birds and reptiles came from the diapsids and the mammals came from the synapsids. he archosaurs (includes dinosaurs and birds) appear in the fossil record 250 Ma, followed by true mammals (225 Ma) and squamates (200 Ma).

This section focuses on the DNA changes that took place in the development of legs that allowed the progression from fish to amphibians, the development of the hard-shelled amniotic egg that allowed reptiles to move to land, and the development of wings that allowed flight in birds. 

The fossil record of the Late Paleozoic and Mesozoic shows that vertebrates went from the sea to land to sky. Three important changes were evolution of legs from fins, evolution of lungs that could breathe in air, and evolution of wings from legs.

The transitions began with the evolution of amphibians from fish. Based on observed fossils during the transitionary period, lobe-finned lung fish began to walk in shallow water in order to evade predators in deeper water. In addition to evidence of transitional amphibians (Section 10-2), there are several modern and fossil lungfish with legs and lungs, from this period and afterwards, such as Dipterus (Figure 10E-3 and 10E-4). As a result, they developed muscular fins with appendages and the ability to breath in air, and they eventually started walking on land because there was an advantage to being able to access food on land (Section 10-2). An example of a living fossil that can breathe out of water and walk on its two legs is Neocerotodus, the Australian lungfish (Figure 10E-6).

The transitions from lungfish fins to amphibian legs have been identified in the fossil record and in DNA. Varga and Varga identified the progression in the fossil record and in modern fish of the development of tetrapod limbs (Figure 10E-5).[1] In addition to the observed transitions in the fossil record (Section 10-2), researchers have identified the same Hox gene phases in fins and limbs.[2] Tulenko et al found that HoxD1-9 genes (Section 9-5) causes the initial budding of the vertebrate limb during the early Hox phase (green side in early Hox phase, Figure 10E-5), and then HoxD10-13 genes cause bud outgrowth and formation of limbs during the late Hox phase (yellow side in late Hox phase, Figure 10E-5). [3] These are the same Hox genes, but modified, that God created in the original vertebrate fish. God facilitated the transition to legs in the original design of the Hox gene or possibly intervened. God either allowed for random mutations to change this gene under selection pressure, or God specifically modified the gene in the Devonian to facilitate the change.

In Figure 10E-5, the three upper fins are from toed fish. In the zebrafish, Danio rerio, the posterior Hox gene expression pattern is the same as in limbs of early tetrapods.[4] In addition, “Late-phase Hox expression governs the growth of digits in tetrapod and dermal fin rays as well as in the distal radials in fish.” The next fin, Latimeria is the only living coeleacanth (lobe finned fish between lungfish and tetrapods). Neoceratodus is an Australian lungfish (Figure 10E-6), which first appeared in the fossil record 380 Ma and can breathe in air. Eustenopteron is a prehistoric lungfish (Figure 10E-5) that lived 385 Ma, in the Late Devonian. It had the beginnings of legs and toes. Tiktaalik (Figure 10E-5 and Figure 10-4) had further development of legs and toes. The further progressive development of legs and toes is clear in the fossil record of the evolution of amphibians (Figure 10E-5)

Bird evolution was uncertain until the last few decades. The fossil record shows that the evolution of birds began with small theropods climbing trees and gliding down (Section 10-3). Their fingers extended and formed wings to improve gliding. Eventually, the evolved wings that could power flight, not just enable gliding. Many related avian dinosaurs, such as Tyrannosaurus Rex had feathers, and some had wings, such as velociraptors, which enabled them to glide toward prey. There is a continuity of reptilian to bird morphology, so it appears that the changes took place naturally based on selection pressures. As with the development of limbs from fins, researchers are able to identify wing development from tetrapods in the fossil record (Section 10-3), embryology, and analysis of Hox genes. They have identified the same patterns of Hox D gene expression and similar initial formation of bird wings and feet and tetrapod feet (Figure 10E-8).[7] [8] [9] It appears that God allowed for the development of bird wings in the original Hox genetic system in the original created vertebrate. The fossil record now shows a plausible sequence for natural bird evolution. 

Although they look different on the surface, the structure of the forelimbs in humans, birds, and bats are similar (Figure 10E-9). The same late phase HoxD genes cause the growth of the three types of forelimbs, carpals, metacarpals, and phalanges (Figure 10E-8). God allowed for the changes in forelimb and wing structure in the HoxD genes that God created in the original vertebrate. God designed the Hox system so that early and late phases of Hox gene expression would first cause the initial budding of the limbs and then the late phase would cause the extension of the limbs and feet.

Brain size is generally correlated with body size, but there are exceptions. Contrary to the popular expression, bird brains are generally 10 times larger than reptile brains per body size, as are mammal brains.[13]  Birds and mammals have large forebrains in comparison with reptiles. The bird forebrain enhances vision.[14] The human forebrain is also engaged in sensory processing, as well as speech and thought. In humans, it is involved in speech. The size of the brain relative to body size is called encephalization. As shown in chapter 6, several genes caused brain expansion. God may have caused some of these changes since a large brain was not necessarily an evolutionary advantage for humans.

Although not every animal is represented since animals appeared in different parts of the world, the Grand Canyon and the Colorado Plateau (Section 3-4) contains the local geologic record and partial fossil record of almost the entire 500 million years of the Phanerozoic Eon. Section 3-4 describes the many geologic formations across the plateau and their methods of deposition. Sections 3-5 and 3-6 describe the evolution of crocodiles and dinosaurs, respectively. One of amazing formations in the Colorado Plateau is Petrified Forest National Monument, which contains a record of the early Triassic and has many Crocodylomorpha fossils (Section 3-5). Dinosaur National Monument (Section 3-6) in the Morrison formation of the Colorado Plateau contains a record of Jurassic dinosaurs. Although some people might struggle with the concept of evolution in general, it is reasonable for most people who struggle with this concept to study the fossil record, which shows gradual change.

Charles Hodge, a highly influential theologian in the latter half of the 19th century, opposed evolution, as presented by Charles Darwin and Thomas Huxley. Hodge’s objection was that Darwin attributed "all the infinite diversities and marvelous organisms of plants and animals … are due to the operation of unintelligent physical causes." Darwin thought that evolution was random and that there was no planned outcome; however, if God created the first vertebrate, which had the demonstrated capacity to evolve legs, wings, large brain, and other essential vertebrate characteristics, then God planned the evolution of fish, reptiles, and mammals, and eventually humans. Hodge was correct to oppose the philosophical perspective of Darwin and Huxley. [15] Unfortunately, Hodge and others tied their objection to the philosophical position of Darwin and Huxley, but they did not appreciate that the details of natural selection were correct. Thus began the long and protracted controversy between the church and science.

Many Christians feel at a gut level, or think from philosophical perspective, or consider from a scriptural perspective, that humans and other animals could not naturally evolve based on random chance in a meaningless and unplanned universe. They are correct. If the first vertebrate was created by God, then we humans would not have naturally evolved from cells or invertebrates. Instead, the vertebrate life system is extremely complex and did not have a natural origin. It is intelligent design at the highest level. If philosophical naturalists would like to contradict this position, then they should begin by showing a natural origin of the vertebrates, which is impossible at this time. If God created the first vertebrate, then there is no philosophical importance in showing natural evolution since the first vertebrate. Without the first vertebrate, life on earth might consist of plants, insects, crabs, worms, mollusks, and other lower animals.

Guyot and Morton debate the fifth day

Guyot claimed that there were birds in the Mesozoic (Age of Reptiles). Morton had the following comments about Guyot’s birds in the Mesozoic, which is somewhat humorous in hindsight.

‘But what will be thought of his rendering of the science account, when we know that there is not the least evidence of the existence of birds properly so called in the period referred to, nor until long afterwards, and that Professor Guyot himself admits as much in the text of this book (pp. 113, 114), but is satisfied with pointing to the "bird-like affinities" of the family of the Dinosaurs (Lizards who stood upon their hind legs like kangaroos), to the bat-like Pterodactyls and bird-like reptiles with teeth, which "prepared the transition to the true birds, which made their appearance, in small numbers, at a later time....To what lengths will devotion to a theory carry a learned, honorable, and devout man!" [16]

Although Morton mocked Guyot’s claim of birds in the Mesozoic, modern science confirmed that birds evolved in the Mesozoic Era. Once again, a pillar of the 19th century argument against the day-age interpretation has been shown to be due to the immaturity of the science of natural history in the 19th century.

Days (Eons) of Our Lives             Episode 3

Mike the Mollusk
Carol the Crocodile

Carol: Mike, I'm surprised you are still here. Its already the Mesozoic.

Mike: Are you surprised that I'm in this episode of the play or that I still exist? You thought I would be written out of the play? Just to let you know, I 'm everyone's favorite phylum. Everyone likes a mollusk.

Carol: I don't think popularity has anything to do with it. I'm everyone's least favorite animal.

Mike; Well, what do you expect? You are an ambush hunter. Everyone has to worry about you every time they go to drink water.

Carol: I realize its not very popular, but it is a great lifestyle. You just sit in the water and every few weeks or months, you leap out and grab an unsuspecting dope. I'm just helping with natural selection.

Mike: I don't know if you know this, but I slithered onto onto the land and became land snails and slugs.

Carol: talk about disgusting. Most people think slugs are the most disgusting animals on earth. Do you have to leave a trail of slime?

Mike: there was an ecological niche there and we evolved into it. Its not our fault. Its just how the world works.

Carol: Well, I just want you to know that we crocodiles are very important. We and the birds are the only archosaurs to make it into the modern world. Thus, all archosaurs, which includes the dinosaurs, are classified as crocodiles or birds.

Mike: We slugs and land snails also made it into the modern world, and like I said, we are the most popular animals, mostly due to our cute shells in marine mollusks.

Carol: Unfortunately, almost nobody, except reptile lovers, likes any crocodilians. Most people wonder why we even exist.

References

[1] Varga, Zsombor, and Máté Varga. "Gene expression changes during the evolution of the tetrapod limb." Biologia Futura 73, no. 4 (2022): 411-426.

[2] Tulenko, Frank J., and Peter D. Currie. "Bones of contention: skeletal patterning across the fin-to-limb transition." Cell 184, no. 4 (2021): 854-856.

[3] Tulenko, Frank J., Gaius J. Augustus, James L. Massey, Seth E. Sims, Sylvie Mazan, and Marcus C. Davis. "HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution." Scientific reports 6, no. 1 (2016): 22720.

[4] Varga and Varga, gene expression.

[5] Starck, J. Matthias, James R. Stewart, and Daniel G. Blackburn. "Phylogeny and evolutionary history of the amniote egg." Journal of Morphology 282, no. 7 (2021): 1080-1122.

[6] Tian, Xin, Joel Gautron, Philippe Monget, and Géraldine Pascal. "What makes an egg unique? Clues from evolutionary scenarios of egg-specific genes." Biology of reproduction 83, no. 6 (2010): 893-900.

[7] Galis, Frietson, Martin Kundrát, and Johan AJ Metz. "Hox genes, digit identities and the theropod/bird transition." J. of Experimental Zoology Part B: Molecular and Developmental Evolution 304, no. 3 (2005): 198-205.

[8] De Bakker, Merijn AG, Wessel van der Vos, Kaylah de Jager, Wing Yu Chung, Donald A. Fowler, Esther Dondorp, Stephan NF Spiekman et al. "Selection on phalanx development in the evolution of the bird wing." Molecular Biology and Evolution 38, no. 10 (2021): 4222-4237.

[9] Vargas, Alexander O., Tiana Kohlsdorf, John F. Fallon, John VandenBrooks, and Günter P. Wagner. "The evolution of HoxD-11 expression in the bird wing: insights from Alligator mississippiensis." PLoS One 3, no. 10 (2008): e3325.

[10] Benson, Roger BJ, Richard J. Butler, Matthew T. Carrano, and Patrick M. O'Connor. "Air‐filled postcranial bones in theropod dinosaurs: physiological implications and the ‘reptile’–bird transition." Biological Reviews 87, no. 1 (2012): 168-193.

[11] Machado, João Paulo, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O’Brien, and Agostinho Antunes. "Bone-associated gene evolution and the origin of flight in birds." BMC genomics 17, no. 1 (2016): 1-15.

[12] Griffin, Christopher T., Joao F. Botelho, Michael Hanson, Matteo Fabbri, Daniel Smith-Paredes, Ryan M. Carney, Mark A. Norell et al. "The developing bird pelvis passes through ancestral dinosaurian conditions." Nature 608, no. 7922 (2022): 346-352

[13] Font, Enrique, Roberto García-Roa, Daniel Pincheira-Donoso, and Pau Carazo. "Rethinking the effects of body size on the study of brain size evolution." Brain Behavior and Evolution 93, no. 4 (2019): 182-195.

[14] Balanoff, Amy M., Gabe S. Bever, Timothy B. Rowe, and Mark A. Norell. "Evolutionary origins of the avian brain." Nature 501, no. 7465 (2013): 93-96.

[15] Hodge, Charles, Systematic Theology. Vol. 2, 12-14.

[16] Morton, President Henry. "The cosmogony of Genesis and its reconcilers." Bibl. Sacra 54 (1897): 27.

Banner

Gansus yumenensis (modern bird) fossil specimen. Beijing Museum of Natural History.  Credit Jonathan Chen. Used here per CC BY-SA 4.0.