Can Amphioxus Shed Light on the Origin of Our Brain?

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by Dr. Elizabeth Mitchell on July 30, 2017
Featured in Answers in Depth


The ancestral amphioxus mused, “If I only had a brain, I could see!” and like magic the evolution of the vertebrate brain was off to the races. This is the latest evolutionary just-so-story of how we got a brain.

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  • Amphioxus is an invertebrate with some features resembling vertebrate embryos.
  • Similar genes regulate the earliest division of the amphioxus and vertebrate embryonic brains.
  • Amphioxus research suggests that some regions of the vertebrate brain classically thought to develop within the embryonic forebrain actually develop from the midbrain. This includes a region vital for survival-enhancing visual reflexes.
  • Evolutionary researchers believe that observable embryonic development holds the key to understanding unobservable evolutionary development of increasingly complex anatomical structures in different kinds of animals. This is called Evo-Devo.
  • Evo-Devo is based on false assumptions.
  • Common designs in different kinds of organisms are consistent with the fact that all share a common Designer, the Creator God of the Bible.

Evolutionary scientists often ponder how the human brain came to be so big—and we explored that question in “One Small Step for DNA, One Giant Leap for Man’s Brain.” But evolutionists also think a lot about the bigger picture: how did any complex vertebrate brain develop in the first place?

Naturally they expect to find the answer at the bottom of the vertebrate family tree, where some shared primitive ancestor of all vertebrates started up the road to braininess. And what creature might be a good stand-in for this simplest possible almost-vertebrate? The lowly amphioxus. Amphioxus is the most studied animal in laboratories comparing vertebrate and invertebrate anatomy.


The amphioxus, also called the lancelet, may be familiar to you—particularly if you went to grade school as long ago as I did—as a brainless faceless fish. Long seen as a link between vertebrates and invertebrates, amphioxus is not, however, a fish. Fish are aquatic vertebrates with gills.


This amphioxus (aka lancelet) specimen is Branchostoma lanceolatum. Amphioxus has a nerve cord with an enlarged area on one end. Amphioxus and vertebrates use similar genes to regulate initial nervous system development in the early embryo. With a simple brain more complex than once thought, the genoarchitecture of its embryonic development may shed light on human embryonic brain development. Image: Hans Hillewaert. Image by © Hans Hillewaert / CC BY-SA 4.0, via Wikimedia Commons.

About two inches long, amphioxus has gill slits instead of gills. It lacks paired fins but has a single fin looping over the top and bottom of its wormlike body. It is found in shallow warm waters worldwide, often buried in sand, where it filters food from the water using its jawless mouth and ciliated gill slits. Amphioxus has no real eyes—just a single light sensor on its head end.

This little nonfish is harvested in Asia as food for man and beast. Moreover, amphioxus has a corresponding cousin in Cambrian rock. Therefore, amphioxus is considered a living fossil and is thought to resemble the last common ancestor that vertebrates and invertebrates presumably shared 520 million years ago.

A Spineless Living Fossil

Amphioxus does not have a spine, which is what we call our bony vertebral column. (That’s why amphioxus is classified as an invertebrate.) But it does have a dorsal nerve cord—a hollow nerve cord running along its back. The dorsal nerve cord resembles the embryonic forerunner of the vertebrate brain and spinal cord. Just beneath this nerve cord is a stiff but flexible non-bony rod called a notochord. The notochord is present in both the larval and adult forms of amphioxus. Vertebrates also develop notochords but only temporarily, during their embryonic development. The vertebrate embryonic notochord helps in the organization of nearby structures, and parts of it are incorporated into the mature vertebrate spine. Because amphioxus has a notochord—resembling the vertebrate embryonic notochord—and a dorsal nerve cord—resembling the vertebrate spinal cord—evolutionists see it as a link between vertebrates and invertebrates.

Amphioxus is not, as once thought, brainless. Its dorsal nerve cord has some regionalization at the head end with distinctive portions corresponding to a forebrain and a hindbrain.1 Furthermore, unlike most invertebrates, embryonic amphioxus develops what brain it has through regionalization of a neural plate. This is also the way vertebrate embryos develop their brains. This similarity goes beyond the anatomical development, as similar genes also regulate the initial division of the amphioxus and vertebrate nervous systems into distinct regions. Therefore, by comparing the embryonic development of the amphioxus nervous system to that of vertebrates like us, scientists hope to get a better understanding of the way the human brain develops at its earliest stages. After all, many anatomical and genetic similarities—aka homologies—exist between humans and many animals. This is not unexpected since we were all engineered by our common designer, the Creator God of the Bible.

But evolutionary scientists interpret such homologies differently. They believe some homologies are evidence that the same useful feature can evolve independently multiple times in diverse, essentially unrelated kinds of animals.2 (This is called convergent evolution.) However, they see many other homologies as evidence of an ancestral relationship between different kinds of organisms on an evolutionary tree of life.3 Further, like 19th and 20th century evolutionists who erroneously believed that embryonic development of vertebrates recapitulates—or replays—their shared evolutionary history, 21st century evolutionists accept a more refined form of this discredited belief. This is called Evo-Devo.

Evo-Devo is the belief that comparative embryology reveals how long ago evolutionary magic occurred.

Evo-Devo is the belief that comparative embryology reveals how long ago evolutionary magic occurred. It is the notion that embryonic development of particular anatomical structures recapitulates the evolutionary development of those structures. In other words, evolutionary researchers still believe that observable embryonic development holds the key to understanding unobservable evolutionary development of increasingly complex kinds of organisms over millions of years. The difference between current thinking and the thinking of those who espoused Ernst Haeckel’s fraudulent claims is that modern proponents of Evo-Devo see evolution through embryology, one organ at a time.

Evo-Devo of the Brain

With its many vertebrate-like features, amphioxus is an “obvious” link between invertebrates and vertebrates for those who believe they must be linked by a shared evolutionary ancestor. Therefore, amphioxus embryos have been the subjects of a recent study4 offering startling revelations about the complexity of the amphioxus brain and the way it develops.

The study was the joint venture of scientists at several Spanish institutions. “We set out to understand what the brain of the cephalochordate amphioxus was like,” explains one of the researchers, José Luis Ferrán. “It is a very simple invertebrate organism, albeit very close to us in evolutionary terms, therefore it gives us some insights as to what our ancestors might have been like. Hence, by comparing the territories of the modern vertebrate brain to that of amphioxus, we analysed what might have occurred to lead them to multiply and how such a complex structure was formed in the course of our evolution.”5

The scientists’ discoveries about the amphioxus brain have revealed a possible error in our understanding of the embryonic developmental stages of human and other vertebrate brains. That might help us better understand some developmental abnormalities. Though this has nothing to do with evolution, the researchers see their findings as an evolutionary roadmap revealing how the vertebrate brain began evolving in the first place.

The Dance of the Embryonic Brain

Let’s take a closer look. In vertebrate embryos—including human embryos—the central nervous system starts out as a thickened neural plate. That flat collection of cells then develops elevated folds on the sides, and those sides roll in to form a neural tube. Choreographed and directed by their genes, cells continue to multiply and differentiate until the head end of this neural tube develops three enlarged regions known as the forebrain, midbrain, and hindbrain. In each region growth and differentiation continue until a vast array of interconnected and interdependent structures develop, ultimately able to produce the most complex structure in the world, the human brain.

This sort of information could have an impact on our understanding the constellations of problems in human brain diseases and developmental abnormalities.

Embryologists have a pretty good idea of which long list of structures develops from each of the three original regions of the neural tube. However, amphioxus brain research now suggests they might be wrong about a couple of these. Two brain regions thought to develop from our forebrain (the thalamus and pretectum, in case you were wondering) may develop from our embryonic midbrain instead. This sort of information could have an impact on our understanding the constellations of problems in human brain diseases and developmental abnormalities. According to Manuel Irimia of Barcolona’s Centre for Genomic Regulation and a lead investigator in this study, the improved map of the amphioxus brain may “help to explain why both the composition and the function of a region are altered. For example, it could lead us to a better understanding of brain-related diseases and why some regions are affected jointly and others are not.”6


An organism’s genes contain the instructions for its embryonic development. And those genes include regulatory genes that switch other genes on and off at just the right time and place as an embryo develops. Many regulatory genes have similar—homologous—forms in a wide range of very different kinds of embryos.

Genoarchitecture determines which genes regulate the formation of the various parts of an embryo. Ferrán, Beatriz Albuixech-Crespo, and their colleagues compared the genoarchitecture of amphioxus and vertebrate embryos. They believe that such comparative genoarchitecture sheds light not just on the way a human embryo’s brain develops in the present but also on the way the human brain evolved from its supposed earliest evolutionary origins.

“In this study, we used genoarchitecture as our main experimental framework to determine the regionalization of the amphioxus neural tube and compare it to that of vertebrates,” explains lead author Beatriz Albuixech-Crespo. “Within this framework, we generated a molecular map of gene expression patterns in amphioxus, whose homologs are known to be involved in establishment and regionalization of the vertebrate brains.”7

Forebrain, Midbrain, and Hindbrain

Let’s take a look at the overall brain plan of the amphioxus and the typical vertebrate embryo to see what genoarchitecture revealed. Amphioxus has only a two-region brain, as compared to the three-region brain seen in the vertebrate embryo.8 One of these regions in the amphioxus can be called the “Di-Mesenscephalic primordium,” a term coined by the researchers. (The other part is the hindbrain.) This new word is made from parts of two other words—diencephalon and mesencephalon. The diencephalon is the lower part of the embryonic vertebrate forebrain. The mesencephalon is the embryonic vertebrate midbrain. The researchers named the top part of the amphioxus brain after these two vertebrate brain parts because the same genes regulate their development and the development of this amphioxus brain part.9 Classic understanding of vertebrate embryology has long held that the thalamus and pretectum develop from the embryonic forebrain, specifically the diencephalon. This genetic switching discovery, if affirmed by further studies in vertebrate embryos, may lead to a revision in human embryology textbooks, tracking the thalamus and pretectum back to the embryonic midbrain instead.

Remember, the researchers made up this name for a midbrain-like region of the amphioxus brain—Di-Mesencephalic primordium—because the genes that regulate its development correspond to the lower end of the vertebrate forebrain (the thalamus and pretectum) as well as the vertebrate midbrain.10 But they still consider the amphioxus brain to have just two divisions. And they note that similar genes regulate the division of both the amphioxus and vertebrate brain initially into two divisions. They assert that this is a reflection of a shared evolutionary past at the deepest level of brain development. Then, they say, additional, secondary signaling genes would have had to evolve to take the organizational differentiation to the next evolutionary level of complexity for vertebrates. “The three classic vertebrate cerebral regions (thalamus, pretectum and midbrain) would have emerged evolutionarily through the action of molecular signalling centres that lead to the expansion and division of a DiMes-like portion,” explains co-investigator Manuel Irimia.11

In Your Mind’s Eye

What could have spurred the evolution of a bigger better brain, one with a real midbrain? The research group believes “the better to see you with, my dear” is the answer. One of those brain parts they now suggest develops as a part of our midbrain rather than the forebrain is the pretectum. (You probably did not know that you have a pretectum, but you do.) The pretectum is the part of your brain that mediates subconscious behavioral responses to sudden changes in light intensity, such as pupillary reflexes that cause our pupils to constrict in bright light. Because such visual reflexes are the most basic visual abilities for survival, they are considered primitive.

Amphioxus does not have eyes like ours, but it does have a single light-sensitive pigment cup on top of its “head.” This frontal “eye” sends signals to the part of its brain that corresponds to our pretectum. Therefore, the researchers believe that the survival value of primitive visual reflexes led to the eventual evolution of this important region of the vertebrate midbrain, making midbrain expansion the key to higher brain development. “The brain has not evolved in isolation, but rather through the interaction of these primitive animals with the environment,” explains University of Murcia’s José Luis Ferrán.12

Is Evo-Devo Valid?

Comparison of the genes that regulate amphioxus and vertebrate embryonic brain development shows that similar genes regulate the division of the amphioxus embryo’s brain into a couple of major divisions and the initial division of the vertebrate embryo’s brain into a couple of divisions. Further differentiation of the vertebrate brain, under the influence of different genes, produces three major regions. This blueprint of early embryonic brain development is a common design found in all vertebrates. From these three regions the most complex structure in nature—the human brain—develops. The latest amphioxus research suggests that a couple of brain parts commonly thought to originate from the forebrain may instead be derivatives of the midbrain.

Scientific observations have never shown any way that one kind of organism can acquire the genetic information to evolve into a new different kind of organism.

But does this information have anything to do with evolution? No. Embryonic development within a particular kind of organism is regulated by that organism’s genome. And it makes sense that embryos develop from the simple to the complex as they grow and differentiate in accordance with the information in their own genome. The existence of many common designs in different kinds of organism—whether genetic, anatomic, or biochemical—is consistent with the fact all share a common designer, the Creator God of the Bible. But scientific observations have never shown any way that one kind of organism can acquire the genetic information to evolve into a new different kind of organism. Not even if seeing better means surviving better!

Proponents of Evo-Devo fool themselves into believing observable comparative embryology is scientifically testable evidence for molecules-to-man evolution. However, Evo-Devo is based on false assumptions, including the belief that an organism is able to acquire the genetic information to become a completely different kind of more complex organism. The common use of similar regulatory genes in different kinds of organisms does not make this leap possible.

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2017 Volume 12


  1. Some scientists have described in amphioxus a small midbrain-like region, essentially a part of the forebrain, that receives input from its frontal eyes. (See Simona Candiani et al., “A Neurochemical Map of the Developing Nervous System,” BMC Neuroscience 13 [2012]: 59, doi:10.1186/1471-2202-13-59; and Linda Holland, “The Origin and Evolution of Chordate Nervous Systems,” Philosophical Transactions of the Royal Society B 370 [2015]: 20150048, doi:10.1098/rstb.2015.0048.) However, the authors of the recent PloSOne Biology study “Molecular Regionalization of the Developing Amphioxus Neural Tube Challenges Major Partitions of the Vertebrate Brain” consider this midbrain-like region to be a subset of the forebrain and call it the Di-Mesencephalic primordium.
  2. Evolutionists do, of course, believe that all living things share a common ancestor if you go back far enough. But the idea of convergent evolution is that after various lineages diverged from one another, the same anatomical features evolved independently in these divergent lines.
  3. Evolutionists believe that some homologous structures are similar forms of a structure that evolved early, in the common ancestor of several lineages, before those lineages diverged.
  4. Beatriz Albuixech-Crespo et al., “Molecular Regionalization of the Developing Amphioxus Neural Tube Challenges Major Partitions of the Vertebrate Brain,” PLoS Biology 15, no. 4 (2017): e2001573,
  5. “New Study Revises the Development and Evolutionary Origin of the Vertebrate Brain,”, April 28, 2017,
  6. “New Study Revises the Development and Evolutionary Origin of the Vertebrate Brain.”
  7. Ibid.
  8. Some other researchers think that amphioxus has a “possible midbrain,” or at least a midbrain-like region. (For instance, see Simona Candiani et al., “A Neurochemical Map of the Developing Nervous System,” 59; and Linda Holland, “The Origin and Evolution of Chordate Nervous Systems,” 370.) This small region is included in the division termed “Di-Mesencephalic primordium” by the authors of the 2017 study in PLOS Biology.
  9. Albuixech-Crespo et al., “Molecular Regionalization of the Developing Amphioxus Neural Tube Challenges Major Partitions of the Vertebrate Brain.”
  10. The third part of the name, primordium, can refer to an evolutionary origin or simply the earliest stage of observable development, such as development in an early embryo.
  11. “New Study Revises the Development and Evolutionary Origin of the Vertebrate Brain.”
  12. Ibid.


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