9E God Created the Vertebrates (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 excursuses in first 12 chapters are my updates to a popular interpretation of the first chapter of Genesis in the 19th century: the day-age interpretation of Arnold Guyot. 

Evidence from Moses and science that God created vertebrates

This section shows why it is reasonable to think that God created the original vertebrate and how God might have been involved in some transitions in vertebrate evolution. After stating that the seas brought forth invertebrates (v. 20), Moses indicated that God created the vertebrates.

Genesis 1:21 (And) God created the great sea monsters and every living creature that moves, with which the waters swarmed after their kind, and every winged bird after its kind; and God saw that it was good.

Why suppose that Genesis 1:21 specifically describes the creation of vertebrates. The first animal is hattannînim haggĕdōlîm. Tannînim means “monster,” and gĕdōlîm means “great.” Tannînim probably comes from a root word that means “to elongate.” The complete phrase is only used one other time in the Bible (Ezekial 29:3). "Speak and say, “Thus says the Lord GOD, ‘Behold, I am against you, Pharaoh king of Egypt, the great monster that lies in the midst of his rivers, that has said, “My Nile is mine, and I myself have made it.”. Almost all commentaries state that the meaning of hattannînim haggĕdōlîm in Ezekiel is crocodile. Whether the meaning is crocodiles or not, vertebrates are large and generally elongated animals. This was an appropriate animal to list on the 5th day since the dominant animals in the age of reptiles were "those archosaurs closer to crocodiles" and "those archosaurs closer to birds," which included dinosaurs. 

The second class of animals in v. 21 is “every living creature that moves, with which the waters teem.” The word translated as moves is haromset. Although there are several interpretations, the Cambridge Bible for Schools and Colleges states, “The Hebrew word denotes the gliding, swift movement of the fish.” The third class of animals in v. 21 is birds. The phrase translated as birds in v. 21, op ka nap, means winged birds and always refers to vertebrate birds and never to insects; thus, all the animals in vs. 21 were vertebrates, and the animals of v. 20 were invertebrates.

There was no “and it was so” or “God saw that it was good” at the end of v. 20; thus, there is no need for the creation of v. 21 (517 Ma) to have taken place after the time of the appearance of insects on land (420 Ma). Thus, God’s command in v. 20 did not need to be fulfilled before the creation of vertebrates took place in v. 21. 

Just as God created the universe in the beginning and then allowed natural processes or a combination of natural processes and divine interventions to form the materials and space from our solar system formed, God initiated the creation of the vertebrates with a spectacular creation at a point in time and then used natural processes to complete the work. It is also possible that God periodically intervened such as mutation of noncoding regions of Hox genes.

Corresponding with Moses’ indication of God’s creation of the vertebrates, paleontologists have no explanation for the sudden appearance of a vertebrate fish in the fossil record of the Cambrian, nor of any of its advanced sensory systems, brain, nervous system, body plan, and organs. In 2018, Henry Gee, senior editor of Nature Journal and expert in vertebrate evolution and physiology, made the following statement.  

“At first sight, many of the characteristic features of vertebrates appear to have evolved all at once. This explains why vertebrates appear so different from anything else in the animal world. However, it is legitimate to ask whether the apparently unique features of vertebrates evolved not simultaneously, but one at a time, and, if so, in which order; and whether some of them might be found, even if in some more modest form, among invertebrates.”  [1]

Homology refers to links between one organism and another through conceivable evolutionary processes or through observed transitions in the fossil record. Although there were some homologous characteristics (Section 9-2) such as a body plan related to other deuterostomes, the advanced vertebrate characteristics were completely nonhomologous (Section 9-3).  Table 9E-1 lists the vertebrate characteristics of the first vertebrate fish that are nonhomologous (no evolutionary connection) with any invertebrate, let alone the Early Cambrian fossil record. 

Table 9E-1. Uniquely vertebrate characteristics for which there is no evidence of homology (linked to a previous organism through an evolutionary process) with any modern invertebrate, let alone the invertebrates of the Early Cambrian.

Nonhomologous Characteristics of the vertebrates

1. Internal skeleton

2. Head (cranium, pharyngeal arches, muscle, cartilage)

3. Eyes (image forming, shape shifting lens, adjustable pupil, ciliary body, skeletal muscles, transparent nerve layers, rods and three types of cones for color vision, optical nerves)

4. Ears (hearing is unique to vertebrates, inner and middle ear)

5. Nose (olfactory placode, olfactory receptors, amygdala)

6. 4 Hox gene clusters

7. Hydroxyapatite

8. Kidney

9. Heart-kidney system

10. Two-chambered heart

11. Neural crest (neurulation, stem cell migration, four parts: cranial, trunk, vagal, and cardiac)

12. Vertebrate muscular system (clock and wave front muscle formation)

13. Complex nervous system

14. Endothelium (possible)

15. Adaptive immune system (possible)

16. Large brain

17. Myelin sheaths around nerves (100X faster than invertebrates)

18. Melanocytes

19. Neuroendocrine cells

20. Sympathetic nerve system

21. Parasympathetic nerve system

22. Central nervous system

23. Nerves (olfactory, optic, oculomotor, trochlear, trigemal, abducens, facial, auditory, glossopharyngeal, vagus, accessory, and hypoglossal)

24. Pituitary gland

Although intelligent design as a concept is valid, this is a case where there is a clear gap in the fossil record between an organism with many complex components and any previous organism. Refer to section 9-7 for a discussion by leading paleontologists about the concerning paleontological problem associated with this gap.

Until 2021, scientists thought that lampreys were basal vertebrates because the larval phase of the lamprey resembles a modern cephalochordate, which would indicate homology between a vertebrate and a primitive invertebrate; however, the basis of the common evolutionary origin was recently disproven by a study of lampreys in the Devonian, which did not have a larval phase.[2] The larval phase of the lamprey evolved at least two hundred million years after the origin of the vertebrates. Frogs have a similar larval phase (tadpole) so the evolution of a larval phase is not unique to lampreys.  

"Remarkably, we've got enough specimens to reconstruct a trajectory from hatchling to adult in several independent lineages of early lampreys," said Michael Coates, Ph.D, a biology professor at UChicago and co-author of the study along with Rob Gess, Ph.D at the Albany Museum and Kristen Tietjin at the University of Kansas. "They each show the same pattern: the larval form was like a miniature adult." [3] 

"We've basically removed lampreys from the position of the ancestral condition of vertebrates," explains lead author Tetsuto Miyashita, Ph.D, a palaeontologist with the Canadian Museum of Nature. "So now we need an alternative." [4]

The Miyashita study was published in the journal Nature. The study came from the Coates lab at University of Chicago, both of which are highly respected. It included fossils from different parts of the world. With the removal of lampreys at the base of the vertebrates, the first vertebrates might be classified as ostracoderms, which were early jawless fish. 

"After their examination of the fossil record, the researchers now believe that extinct armored fishes known as ostracoderms might instead represent better candidates for the root of the vertebrate family tree, whereas modern lamprey larvae are a more recent evolutionary innovation.” [5]

Although scientists had worked hard to identify homologous characteristics of vertebrates and modern cephalochordates in order to identify the origin of the vertebrates, the problem is that the modern cephalochordates did not exist in the Cambrian. They are just degenerate lampreys that evolved after the Devonian period, long after the first vertebrate fish. God began with a different invertebrate to create the vertebrates. For example, there are several homologous genetic and physiological characteristics in vertebrates and annelid worms.  

Based on morphological similarities between vertebrates and some early fossilized organisms such as Pikaia and genetic similarities with early annelid worms (Section 9-5), it is likely that God adapted an existing organism from the Early Cambrian to create the vertebrates. Figure 9E-1 shows a hypothetical scenario for God’s creation of the vertebrates.

It seems that the selection pressure for fins was due to the need to optimize swimming. Donoghue and the research team simulated the flow of water over the fish with the “paired body wall extensions.” The simulations showed that the fins gave an advantage in swimming.

“The results of our CFD experiments also suggest that, irrespective of a debate regarding their homology, the prevalence of diverse paired body-wall extensions in jawless stem gnathostomes reflects widespread adaptation to passively generating lift before the origin of muscularized paired fins.” [9]

The question is whether God modified DNA to form the fin folds or whether natural mutations in DNA led to the fin folds. One way to determine that a cause was natural was that it occurs over and over. The fin folds in the Galeaspid were not the first fins in the fossil record; Fins or fin folds evolved multiple times because they increased swimming efficiency.[10] Figure 9E-5 shows the progression of various fin structures in Paleozoic fish, including their own fossil, Tujiaaspis.

As will be shown in section 3-1, the evolution of fins and finally limbs in vertebrates was governed by the Hox D cluster, which was unique to the original vertebrate fish. If God designed the HoxD cluster, as must have been the case if God created vertebrates, then God programmed the capacity for fin folds into the original DNA of the vertebrate fish.

In summary, the old hypothesis for the origin of fins (Figure 2I-3) was confirmed by an observed fossil and CFD (computed fluid dynamics) simulation that showed the improved swimming efficiency with fin folds. As with the 18th century paleontologists, God would have known that various types of fins and fin folds would optimize swimming efficiency. Thus, God planned on the evolution of pelvic and pectoral fins by allowing for this change in the HoxD cluster.

With respect to the progression of evolution, there were two major groups of genes and gene patterns in vertebrates. Many are nearly the same as and were inherited from invertebrates, but many are unique to the vertebrates, and have no evolutionary connection. Since there is no evolutionary connection and because Moses claimed that God created the vertebrates, the conclusion is that God created the unique genes and patterns of genes in the vertebrates. The following chapters will make the argument that the structural changes such as jaws, fins, legs, and wings, and advances in sensory systems such as tetrapod and bird intelligence and sight, were based on the new genes and organs that God inserted into the original vertebrate.

The common genes and gene patterns are also in cnidarians and annelids and indicate a close evolutionary relationship between vertebrates and invertebrates (Section 2-5). For example, cellular design, neurosecretory genes, neurotrophins, retinoic acid triggers, Pax6 protein (eyes) are in vertebrates and invertebrates. Other genes were amplified in vertebrates, such as the vtg gene in invertebrates became the vtg family of genes in vertebrates. The body patterning Hox genes were amplified in vertebrates. After segmentation genes define boundaries, Hox genes trigger the formation of structures. The single Hox gene cluster in invertebrates, including 13 Hox genes, became four Hox gene clusters in vertebrates (A, B, C, and D).

Hox genes line up in clusters in DNA in the same order with which they trigger the formation of different parts of animals. In the jaw, which is at the anterior end (front) of vertebrates, Hox genes in positions 1 to 3, primarily from the A and B Hox gene clusters govern the formation of the jaw.[11] Thus, even though the original vertebrate fish did not have a jaw, God allowed for the development of the jaw in the noncoding regions of Hox genes. While the coding regions of Hox genes, which govern the formation of many structures, cannot be changed without death or severe disease, the noncoding regions of Hox genes can mutate and cause positive structural changes in organisms. The seminal research on this topic proved that mutations in the noncoding region of the Pitx1 Hox gene caused changes in stickleback fish anatomy.[12]

The same four Hox gene clusters were carried through from fish to reptiles to mammals and birds. (Figure 2-17). There are also an extra three Hox gene clusters in ray finned fish, which evolved through whole genome duplication. Scientists generally attribute the increase from one to four Hox gene clusters in the original vertebrate fish to two whole genome duplications (2R WGD); however, the patterns of the genes in the clusters does not support this conclusion (Section 2-5). In addition, there are new genes in vertebrates, which would not occur with whole genome duplications.  Genome duplication can explain diversity but it cannot explain new functions (Table 2I-1), genes, and molecules.

One of the conceivable possibilities with Hox genes and random mutation of noncoding regions of Hox genes is that new structures might arise. Why weren’t there huge vertebrates that looked like spiders and mollusks? While there are some crazy looking ray-finned fish in the sea with odd appendages, and with 7 clusters of Hox genes, all of the vertebrates on land have zero (snakes) to two sets of paired appendages. Whatever the cause, God’s plan for vertebrates on land who did not slither on the ground is that they would have two sets of paired limbs.

Vertebrates have a known rate of DNA mutation, and this enables scientists to estimate their theoretical time of origin and/or divergence from invertebrates. This calculation is called the molecular clock technique. The calculated time of divergence in invertebrates and vertebrates, based on their genetic difference, has ranged from about 700 million to 1.2 billion years ago. Section 2-7 describes the molecular clock estimates for the origin of the vertebrates and a debate about it between leading paleontologists, most of whom think the origin of animals began with the Avalon Explosion in the Late Ediacaran. Dr. Donoghue, from the University of Bristol and one of the authors of the Tujiaaspis paper, agrees with the other paleontologists that the paleontological record of the Late Ediacaran does not indicate that this ancient vertebrate ancestor, preceding the Avalon Explosion will be found, but he believes that it will be found because he believes that it must be there. This type of belief in an unobserved outcome might sound fanciful, but it is extremely important in paleontology. Paleontologists use these types of conclusions and convictions to guide their search for new fossils. Unfortunately, Dr. Donoghue will be frustrated in his quest because Haikouichthys, or a recent ancestor of Haikouichthys, was a supernatural creation, as Moses stated.

The timing of God’s design of vertebrate evolution within the invertebrate ecosystem was important. God began the process of vertebrate evolution with an organism without a jaw. Although the fish might have been carnivores or omnivores, they were limited in the capacity to attack and devour other organisms. Thus, the fish did not overwhelm the newly emerging invertebrate ecosystem. As vertebrate fish evolved jaws and fins and became much larger and fiercer, the invertebrates evolved methods and mechanisms to survive in this world dominated by the vertebrates. Thus, the evolving ecosystems with vertebrates and invertebrates were sustainable and continued to the present.

God intervened in invertebrate and vertebrate evolution through control of the environment. God changed the environment of the air and seas by changing the tilt of earth’s axis on the fourth day. God also might have controlled, or at least planned on changes in the positions of continents, that led to changes in climate and possibly influenced the environment of the seas.

The following episode of Days (Eons) of Our Lives might help people gain a perspective on some of the concerning issues of early animal evolution.

Days (Eons) of Our Lives             Episode 2

Louise the jawless female vertebrate fish
Fred the jawless male vertebrate fish
Mike the filter feeding Mollusk

Louise: Mike, you just sit there and filter feed. You can't see. You don't have a brain. You can hardly move on the ground, and you can't swim.

Mike: Louise, you are a real vertebracist

Fred: Mike, if she was criticizing another vertebrate such as a Burgess Shalian, then she might be a vertebracist, but you are just an invertebrate mollusk.

Mike: It’s your attitude that is really destructive. Before you guys showed up, basically from I don't know where, everyone was relatively happy. We were moving through the muck, filter feeding, or attacking each other, and everyone just felt like part of the invertegang.

Fred: Mike, it is only going to get worse. Soon we will have jaws and fins, then we will move to land, then we will fly, and finally we will become humans, the pinnacle of creation.

Mike: Not so fast there guy. We are also going to move to land and sky. We will have almost a million species. What do you think about that?

Louise: Aside from the fact that it’s the arthropods and not the mollusks who will dominate the land, you will all be tiny because you don't have a kidney to filter out the impurities. And you call yourself a filter feeder.

Mike: This means war. We are all going to arm ourselves during the Cambrian. Mollusk against mollusk. Mollusk against vertebrate. Mollusk against arthropod. And the war will continue on land and in the sky. Invertebrates will sting you, bite you, transfer diseases to you, squish under your feet, and eat your food.

Fred: These things may be true, but we are going to eat you, cook you, sometimes alive, hit you with fly swatters, drug you and kill you, and make deadly lights.

Mike: What about the Hindus? They are going to live in perfect harmony with us. They would not kill a fly. The permaculture people will also live in harmony with nature. You don't have to kill us.

Louise: Mike, one thing I can tell you is that humans are not going to eat you, maybe just a few invertebrates such as locusts, because Leviticus 11:43 says that all of the swarming things that creep along the ground are unclean.

Mike: Oh that’s just great, you call us unclean. Vertebracist, vertebracist.

Fred: Good by Mike, I am just going to swim over and see some beautiful sea anemones and sponges on a rock ledge. It sure is great being a fish. Aaah. An Anomalocarous just grabbed me.

Mike: Good bye Fred. Pride comes before the fall.

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Original vertebrate fish, Haikouichthys. Credit: Nobu Tomura. CC BY-SA.

References

[1] Gee, Henry, Across the bridge: understanding the origin of the vertebrates. University of Chicago Press, 2018

[2] Miyashita, Tetsuto, Robert W. Gess, Kristen Tietjen, and Michael I. Coates. "Non-ammocoete larvae of Palaeozoic stem lampreys." Nature 591, no. 7850 (2021): 408-412.

[3] Canadian Museum of Nature. "Long-accepted theory of vertebrate origin upended by fossilized lamprey larvae." ScienceDaily. www.sciencedaily.com/releases/2021/03/210310122538.htm (accessed October 19, 2021).

[4] Canadian Museum, Long-accepted.

[5] Canadian Museum, Long-accepted.

[6] DeLaurier, April. "Evolution and development of the fish jaw skeleton." Wiley Interdisciplinary Reviews: Developmental Biology 8, no. 2 (2019): e337.

[7] Gai, Zhikun, Qiang Li, Humberto G. Ferrón, Joseph N. Keating, Junqing Wang, Philip CJ Donoghue, and Min Zhu. "Galeaspid anatomy and the origin of vertebrate paired appendages." Nature 609, no. 7929 (2022): 959-963.

[8] University of Bristol. Dead fish breathes new life into the evolutionary origin of fins and limbs. https://www.bristol.ac.uk/biology/news/2022/dead-fish-breathes-new-life-into-the-evolutionary-origin-of-fins-and-limbs.html. Press release issued: 4 October 2022

[9] Gai, Galleaspid

[10] Gai, Galleaspid

[11] Parker, Hugo J., Bony De Kumar, Stephen A. Green, Karin D. Prummel, Christopher Hess, Charles K. Kaufman, Christian Mosimann, Leanne M. Wiedemann, Marianne E. Bronner, and Robb Krumlauf. "A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates." Nature communications 10, no. 1 (2019): 1189.

[12] Shapiro M. D., M. E. Marks, C. L. Peichel, B. K. Blackman, K. S. Nereng, B. Jonsson, D. Schluter, D. M. Kingsley. 2004. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 439(7079): 1014.