Seventy Percent of Human Genes Traced Back to Acorn Worm?

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Evolutionary scientists claim they have traced the origin of the human throat—and 70% of our genes—back to gill slits and DNA in the lowly acorn worm, “our closest wormy cousin.” Should we swallow it?

In an effort to discover the characteristics we humans supposedly inherited from organisms found in the Cambrian explosion, scientists have sequenced the genome of the acorn worm. “It's an ugly beast,” says UC Berkeley professor John Gerhart, leader of the project. Coauthor Daniel Rokhsar boldly claims, “Acorn worms are marine invertebrates that, despite their decidedly nonvertebrate form are nevertheless among our closest invertebrate relatives.”1

“Acorn worms look very different from chordates, which makes it especially surprising that they and chordates, like humans, are so similar on the genomic, developmental and cell biological levels,” Gerhart adds.2 Chordates include humans and other vertebrates as well as a few invertebrates, but not acorn worms. Chordates, if only as an embryo, have a bundle of nerves like a spinal cord supported by a cartilaginous notochord, a body that extends past the anal opening, and a series of openings in the side of the throat (pharyngeal slits). Reflecting the evolutionary presumptions that guide his interpretation of genetic comparisons, Gerhart says, “I'm interested in the origins of chordates, which, of course, came from non-chordates, and hemichordates like the acorn worm are the closest we have to this lineage. So it’s important to compare the development and genomes of our group, the chordates, with the hemichordates if you want to know what characteristics the common ancestor really had.”3

“The Mouth Forms Second”

Evolutionists think acorn worms, which have not changed significantly since their preservation in the Cambrian fossil record,4 are a living representation of the evolutionary link between vertebrates and invertebrates. All vertebrates and some invertebrates—like acorn worms—are deuterostomes, a word meaning “the mouth is second.” The mouth in deuterostome embryos develops “second”—after the opening for the other end of the digestive tract.5 This “deuterostome” pattern of embryonic development is found not only in acorn worms but also in starfish, sea urchins, fish, and all other vertebrates, including humans. Evolutionary scientists believe that this embryologic pattern is the evolutionary footprint of our shared history with these animals through a common deuterostome ancestor that presumably lived 570 million years ago.6 This genetic study, in the opinion of the authors, confirms evolutionary relationships between these very different kinds of animals, as well as humans.

Of course, the scientists could not actually sequence DNA from a common ancestor of acorn worms and vertebrates—that ancestor being purely hypothetical, existing only in their worldview-based imaginations. Instead, Gerhart, Rokshar, Simarkov, and colleagues sequenced the genomes of two of the 90 or so living species of acorn worms. Oleg Simakov, coauthor of the study in Nature, says, “Our analysis of the acorn worm genomes provides a glimpse into our Cambrian ancestors’ complexity and supplies support for the ancient link between the pharyngeal development and the filter feeding lifestyle that ultimately contributed to our evolution.”7

Genetic Similarities

The authors of the study report that 8,716 genes have similar counterparts (homologues) present in enough diverse deuterostomes to “imply their presence in the deuterostome ancestor.”8 In addition to the discovery that vertebrates and invertebrates like acorn worms share many protein-coding DNA sequences, the authors found that some sections of DNA thought to regulate genetic expression appear in all the different types of deuterostomes they sampled.9 The order in which many genes are arranged is also similar, suggesting that if certain groups of genes work together in one kind of animal they often work together in many different kinds of animals.

The scientists found more genetic similarities between invertebrates than between acorn worms and vertebrates. Yet depending on how the genes are tallied,10 as much as 70% of the human genome’s approximately 20,000 genes (DNA sequences that code for proteins) have counterparts in the acorn worm and hence—by evolutionary reckoning—with the last common ancestor shared with our so-called “closest wormy cousin.”11

Of course, we expect to find many common genes in different kinds of animals.

Of course, we expect to find many common genes in different kinds of animals. They live in the same world in bodies utilizing the same basic biochemistry and sharing many of the same basic needs. And like genes, many different kinds of organisms need the same or similar regulatory elements in their genomes. This does not demonstrate common evolutionary ancestry, just a common Designer—the Creator God.

Furthermore, we are accustomed to hearing that we share about 98% of our genome with chimpanzees—supposedly our closest primate cousin. Such oft-quoted numbers are, as Frost Smith explains in “A Fresh Look at Human-Chimp DNA Similarity,” deceptively impressive. And as Dr. Nathaniel Jeanson points out in “Differences Between Chimp and Human DNA Recalculated,” evolutionists conveniently overlook the hundreds of millions of genetic differences that evolution can never bridge.

Acorn Worm
Acorn Worm Diagram

This is an acorn worm. It has many gill slits—shown in blue in the diagram—allowing water to pass through its mouth and out of its body through gill pores. From this water an acorn worm not only obtains oxygen—as fish do—but also nutritious organic debris. The gill slits filter this food from the water. Photograph by user Necrophorus, via Wikimedia Commons. Diagram by user Zebra.element, via Wikipedia.

Gill Slits—Our Greatest Shared Innovation?

Acorn worms range in size from 3 ½ inches to over 8 feet, and though most species live in shallow brackish water, some live at the bottom of the sea. The acorn worm pokes its acorn-shaped proboscis around in sand or mud, stirring up debris. It directs the debris-laden water into its mouth using cilia and collects not only oxygen but also bacteria, algae, and other nutritious edible organics by filtering it through its pharyngeal slits, or gill slits. An acorn worm can have hundreds of gill slits, equipping it for a very efficient form of filter feeding.

“What’s so great about having gill slits is the large volumes of water you can put through the animal to collect food; they allow high-throughput filtering and feeding, whereas other animals take one gulp, deal with the food in that one gulp, expel the water out the mouth and take another gulp,” Rokhsar explains.12 But the significance of gill slits in this invertebrate goes far beyond these observable advantages to the acorn worm and to an evolutionarily minded scientist speaks volumes about the unobservable past history of many other kinds of animals, and even humans.

Evolutionists believe that gill slits evolved in animals like acorn worms to make filter feeding efficient and then later evolved into oxygen-capturing gills and even later into various parts of our throats that have no direct oxygen-gathering roles at all. As Rokhsar says, “The presence of these slits in acorn worms and vertebrates tells us that our last common ancestor also had them, and was likely a filter feeder like acorn worms today. The pharyngeal area of these worms and of all deuterostomes is their most significant shared innovation.”13

Neither humans nor other mammals have gills at any point in their development.

Neither humans nor other mammals have gills at any point in their development. Human embryos have several swellings along the neck, little mounds of cells that differentiate into parts of the jaw, face, ear, middle ear bones, thyroid and parathyroid glands, and voice box. Based on superficial appearance and evolutionary thinking, these folds and swellings were once called gill slits, gill pouches, gill arches, or branchial arches. Many embryology textbooks have abandoned this deceptive terminology in favor of pharyngeal arches—meaning “arches in the region of the throat.” But the authors believe genetic similarities confirm a gill slit origin for them. That’s why Rokhsar refers to the acorn worm’s gill slits as our “most significant shared innovation.”

Genes for Such a Worm as I

The authors found that a cluster of six genes expressed during formation of the embryonic acorn worm’s gill slits corresponds to a cluster of six genes expressed in a similar anatomical region in many other kinds of deuterostome embryos, including humans. This cluster of genes consists of coding for four transcription factors—proteins that control the rate at which various genes are transcribed (from DNA into RNA)—as well as two common regulatory genes. Though this group of genes is not found in all the deuterostomes they tested, it was only found in deuterostomes, and they “conclude that the deuterostome ancestor possessed such a cluster.”14 They write, “We propose that the clustering of the four ordered transcription factors, and their bystander genes, on the deuterostome stem served a regulatory role in the evolution of the pharyngeal apparatus.”15 Rokhsar says, “We think this is an ancient deuterostome-specific cluster of genes that is involved in patterning the pharynx.”

This gene cluster is one more piece of evidence affirming the reality of the Creator we share with all living things.

Well, Rokshar is right in saying that this gene cluster is involved in patterning the pharynx in many different kinds of deuterostomes—that much is observable! This gene cluster is involved directing the embryologic development of pharyngeal arches into sundry different anatomical structures in the neck region of diverse sorts of invertebrates and vertebrates. But these authors are incorrect in their conclusion that the common presence of this gene cluster confirms that these invertebrates and vertebrates share a common ancestor. On the contrary, this gene cluster is one more piece of evidence affirming the reality of the Creator we share with all living things. This six-gene cluster, of use directing the embryonic development of so many different structures in different kinds of embryos, is not evidence of a shared evolutionary heritage but of a shared Creator.

Do we have acorn worm in our ancestral past? Not at all. Since the same basic biochemistry operates in all living things on this planet, it is not surprising that many genes and non-coding DNA sequences are similar or even identical. The existence of homologous genes, like homologous anatomical structures, does not scream “evolution” but is readily explained by the fact that all things—from molecules to man—were designed by the same Creator God.

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Answers in Depth

2016 Volume 11


  1. Unversity of California – Berkeley, “Acorn Worm Genome Reveals Gill Origins of Human Pharynx,” ScienceDaily, November 19, 2015,
  2. Ibid.
  3. Ibid.
  4. As discussed in “Ancient Fossil Looks Like Today’s Acorn Worms,” the variety of acorn worms found preserved in Cambrian rock by catastrophic burial at the time of the global Flood varied in that they were able to build a tube burrow, an ability apparently lost among today’s acorn worms.
  5. Bilaterally symmetrical animals (such as insects, mollusks, and annelids) in which the embryonic mouth forms before the opening at the other end are called protostomes.
  6. This estimated date for the divergence of chordates and non-chordates (like the acorn worms’ ancestors) from their hypothetical last common ancestor—570 million years—is derived from molecular clock dating. These dates are based on numerous unverifiable evolutionary assumptions, including calibration points derived from the evolutionary interpretation and dating of the fossil record.
  7. Catherine Griffin, “Evolution from Worms: 70 Percent of Human Genes Trace Ancestry to the Acorn Worm,” Science World Report, November 19, 2015,
  8. Oleg Simakov et al., “Hemichordate Genomes and Deuterostome Origins,” Nature (November 18, 2015), doi:10.1038/nature16150.
  9. The study reports the discovery of 6,533 non-coding DNA sections at least 50 base pairs long. (These might have regulatory functions, but that remains to be determined.) While this number may sound high, we should recall that only a tiny fraction (around 2%) of the human genome consists of protein-coding segments (genes). Thus most of the 3 billion base pairs in the human genome are not involved in the blueprints for proteins. (The ENCODE project has shown, incidentally, that we should not think of these non-coding parts of the genome as “junk”! Read more about it in “Decoding the Debris.”) These 6,533 non-coding sections represent a small though significant portion of these. It is likely that, like genes, many different kinds of organisms need the same or similar regulatory and other associated elements in their genomes.
  10. The human genome, like other genomes, contains many genes that structurally resemble genes elsewhere within the genome. These may vary in their DNA sequences by as much as about 10% and have their own functions, but evolutionists—rather than considering them part of the genome’s design—view them as mere “copies” and assume they are evidence that gene duplication provided the raw material through which novel evolutionary functions evolved. In any case, the existence of such structurally similar DNA sequences accounts in part for the rather large percentage of genetic similarity quoted in the paper in Nature. The authors acknowledge this unverifiable evolutionary presupposition, writing, “Owing to gene duplication and other processes the descendants of these ancestral genes account for ~14,000 genes in extant deuterostome genomes including human.” (Simakov et al., “Hemichordate Genomes . . . ”)
  11. Letizia Diamante, “Our Closest Wormy Cousins,” Okinawa Institute of Science and Technology, November 19, 2015,
  12. Unversity of California – Berkeley, “Acorn Worm Genome . . . ”
  13. Ibid.
  14. Note 9, Supplemental Materials for Simakov et al., “Hemichordate Genomes . . . ” doi:10.1038/nature16150.
  15. Simakov et al., “Hemichordate Genomes . . . ”


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