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Did the Origin of Animals Require New Genes?

Photo credit: Smith609 at English Wikipedia / CC BY-SA (http://creativecommons.org/licenses/by-sa/3.0/).

Stephen Meyer recently did an Uncommon Knowledge podcast interview with Peter Robinson of Stanford University’s Hoover Institution about his new book Return of the God Hypothesis: Three Scientific Discoveries That Reveal the Mind Behind the Universe. I took a week off for Easter and read the book during the holiday — it’s another masterpiece from Meyer. He breaks new ground in showing that not only do materialists smuggle in information when trying to explain the origin of biological complexity, but they do the same thing when seeking to explain how the universe arose from “nothing,” or when they appeal to the “multiverse” to explain away cosmic fine-tuning. 

Virtually everywhere we observe the same pattern: information is at the foundation of nature’s complexity, and information requires an intelligent cause. Materialists who purport to explain the origin of that complexity by smuggling in information unwittingly demonstrate the need for intelligent design. That’s Meyer’s argument in a nutshell, but you’ll have to read the book to fully appreciate it. 

Back to Uncommon Knowledge. In a comment below the podcast, self-described “layman” Andrew Baldwin makes an objection to Meyer’s book that we’ve addressed here in the past:

Part of Meyer’s new book and his interview repeats the argument of his previous book, “Darwin’s Doubt”. University of Toronto’s Larry Moran (“Stephen Meyer isn’t keeping up”, August 5, 2014), writes: “Our current model for evolution and development is that small changes in the regulation and timing of key developmental genes are responsible for big phenotypic differences, including new animal body plans. The data shows that all the animal phyla have similar genes and that there aren’t very many genes whose origins can be traced to the Cambrian.” This contradicts what Meyer writes in his book, and says in this interview, and since Moran is the biochemist and Meyer isn’t, a layman like myself would tend to accept Moran’s view. 

I thank Mr. Baldwin for his comment because it provides an occasion for revisiting some key points. That is helpful. I appreciate, too, that sometimes it can be challenging for a layperson to assess the scientific evidence. But it remains vital to think for yourself and not simply accept an argument because some purported authority (in this case, Larry Moran) said it.

It’s interesting that the commenter’s only objection to Meyer is regarding material from his previous book, Darwin’s Doubt, on the evolution of life and the Cambrian explosion. Baldwin has no objections, apparently, to Meyer’s central arguments in Return of the God Hypothesis that the universe’s fine-tuning for life points to a designer.

Many New Genes Necessary for Animal Origins

Meyer and the rest of us have, of course, been “keeping up” closely with the literature on the question of whether Cambrian animals required new genes. The subject came up in Steve’s 2013 radio debate with U.C. Berkeley paleontologist Charles Marshall. When he wrote Darwin’s Doubt in 2013, the data supported Meyer’s view that the origin of the Cambrian animals required new genes. Since then, new papers have come out that have spectacularly affirmed Meyer’s position. We’ll get to that in a moment, but first let’s note that there are many logical problems with the view that Larry Moran espouses.

In his epilogue to Darwin’s Doubt, published in 2014, and in his debate with Charles Marshall, Stephen Meyer explained that at that time, we had very strong reasons to believe that the various animal phyla that appear abruptly in the Cambrian period would have required new genes. As Meyer wrote in the epilogue: 

[T]he evolutionary process would need to produce a whole range of proteins necessary to build and service specific forms of animal life. Indeed, different forms of complex animal life exhibit unique cell types, and typically each cell type depends upon other specialized or dedicated proteins — which in turn requires genetic information. In Chapter 8, “The Cambrian Information Explosion,” I offer numerous examples of this. The first arthropods would likely have required genes for building the complex protein lysyl oxidase (see p. 191). Why? Because what we know from studies of modern arthropods shows that this protein is necessary to support the stout body structure of arthropod exoskeletons. Similarly, the first animals with guts (and epithelial cells lining them) would have required specialized digestive enzymes and specialized regulatory enzymes to control the secretion of those enzymes (see p. 162). Other examples abound. Tunicates require specialized proteins for building their distinctive “tunics.” Mollusks require scores of specialized proteins for building their shells. Indeed, building metazoans at all requires specialized proteins (and metabolic pathways) just to produce the kind of extracellular matrices that allow developing animals to knit cells into tissues, tissues into organs, and organs and tissues into fully developed animals. Our observations of animals representing known phyla that first arose in the Cambrian show that such animals would also have needed other specialized proteins: for facilitating adhesion, for regulating development, for building specialized tissues or structural parts of specialized organs, for producing eggs and sperm as well as many other distinctive functions and structures. Obviously, these proteins must have arisen sometime in the history of life. Since most major metazoan body plans first arose in the Cambrian explosion, it is reasonable to infer that the proteins necessary to sustain those forms of life—and the genetic information necessary to synthesize them — had come into existence by that time. 

(Darwin’s Doubt, p. 444)

Marshall and Moran dismissed these arguments and evidence. They presumed that the animal body plans that arose in the Cambrian did not require any new genes, but came about simply by rewiring gene regulatory networks. In their view, building animal body plans required just changing the expression of pre-existing genes. As Marshall put it in his review of Darwin’s Doubt in the journal Science:

[Meyer’s] case against the current scientific explanations of the relatively rapid appearance of the animal phyla rests on the claim that the origin of new animal body plans requires vast amounts of novel genetic information coupled with the unsubstantiated assertion that this new genetic information must include many new protein folds. In fact, our present understanding of morphogenesis indicates that new phyla were not made by new genes but largely emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes.

Marshall went on to say that Meyer has an “idiosyncratic fixation with new protein folds” and “an outdated understanding of morphogenesis” — all due to Meyer’s supposedly inaccurate claims that the Cambrian explosion would have required the origin of many new genes. But as with Moran, there are many problems with Marshall’s position. 

Pushing Back the Origin of Genetic Information

In addition to citing some of the evidence of unique features of animals that would have required new genes, Meyer pointed out an obvious fact: Marshall has simply pushed the question of the origin of new genes back. Marshall’s proposal does not eliminate the need to explain the origin of genetic information. Rather, he presupposed, but did not explain, several separate sources of pre-existing genetic information.

Second, Meyer pointed out that Marshall’s proposed “rewiring” of gene regulatory networks itself required an infusion of new information. Because known changes to gene regulatory networks are always harmful or deadly (see here for a discussion), it would have required a whole host of coordinated genetic mutations to various regulatory regions in the genome, requiring significant informational inputs. The need to generate multiple coordinated mutations would have faced many of the problems faced by other evolutionary mechanisms that Meyer discusses in Chapter 10 of Return of the God Hypothesis, and Chapter 12 of Darwin’s Doubt.

Regulatory Hox Genes Won’t Explain Body Plan Origins

Larry Moran argues that “small changes in the regulation and timing of key developmental genes are responsible for big phenotypic differences.” One of the primary classes of regulatory genes discovered in animals is known as Hox genes. Meyer explained in Darwin’s Doubt why changes to Hox genes won’t explain the origin of body plans:

Hox genes in all animal forms are expressed aft er the beginning of animal development, and well aft er the body plan has begun to be established. In fruit flies, by the time that Hox genes are expressed, roughly 6,000 cells have already formed, and the basic geometry of the fly — its anterior, posterior, dorsal, and ventral axes — is already well established. So Hox genes don’t determine body-plan formation. Eric Davidson and Douglas Erwin have pointed out that Hox gene expression, although necessary for correct regional or local differentiation within a body plan, occurs much later during embryogenesis than global bodyplan specification itself, which is regulated by entirely different genes. 

(Darwin’s Doubt, p. 319)

Invoking changes to Hox genes won’t solve the problem of generating animal body plans. 

Recent Studies Show “Many” New Genes Necessary for Animal Origins

But there’s another problem that is devastating to the arguments of Marshall and Moran: studies published in the last few years have provided compelling evidence that many — hundreds if not thousands — of new genes would have been necessary for the origin of the animals that appear in the Cambrian explosion. 

In 2018, a paper in Nature Communications by Jordi Paps and Peter Holland, “Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty,” provided a direct refutation of Marshall. The study compared the genomes of modern-day animals to determine what genes they share. The result was then used to determine which genes were present in the genomes of the putative common ancestors of various animal groups. By comparing the common genes shared at different levels of the animal taxonomic hierarchy, they were able to determine how many new genes would have to appear at various stages of animal evolution. They found that the origin of new animal groups would have required hundreds if not thousands of new genes. I covered this paper when it was published. Here’s what it says:

Recent studies show that many genes typically associated with metazoan functions actually pre-date animals themselves, supporting functional co-option of ‘unicellular genes’ during the genesis of metazoans. 

However, the role of genome novelty in animal origins has not been fully evaluated. We hypothesize that genomic novelty had a major impact in this transition, particularly involving biological functions which are hallmarks of animal multicellularity (gene regulation, signalling, cell adhesion, and cell cycle). Here we apply a comparative genomics approach using sophisticated methods, newly developed programs, and a comprehensive taxon sampling. The reconstruction of the ancestral genome of the last common ancestor of animals shows a set of biological functions similar to other eukaryote ancestors, while revealing an unexpected expansion of gene diversity. These analyses also highlight 25 groups of genes only found in animals that are highly retained in all their genomes, with essential functions linked to animal multicellularity. [Emphasis added.]

Jordi Paps and Peter W.H. Holland, “Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty,” Nature Communications, 9 (2018), 1730.

They conclude that “many new” genes were necessary during the origin of animals: 

Thus, the first animal genome was not only showing a higher proportion of Novel HG [homology groups], but these also perform major multicellular functions in the modern fruit fly genome. The implication is that the transition was accompanied by an increase of genomic innovation, including many new, divergent, and subsequently ubiquitous genes encoding regulatory functions associated with animal multicellularity. [Emphasis added.]

These “homology groups” (HGs) are exactly what they sound like — groups of genes that are similar. A “novel HG” is a group of genes that is found in animals, or particular groups of animals, that does not exist elsewhere. This indicates that these groups of genes were necessary for these animals to exist.

How Many New Genes?

How many novel HGs (and genes) are we talking about? The paper is open access. Readers can see for themselves that Figure 1 shows 1189 HGs are necessary for the origin of Metazoa (multicellular organisms with differentiated tissues). However, as one moves farther up the animal tree, hundreds if not thousands of additional novel HGs are required:

  • For the origin of Eumetazoa (sponges, Planulozoa, and Bilateria), 494 novel HGs are required.
  • For the origin of Planulozoa (ctenophores, placozoans, cnidarians, and bilaterians), 1201 novel HGs are needed.
  • For the origin of Bilateria (animals with two-sided symmetry — a left and a right side), an additional 1580 HGs are required! According to Figure 2, about 16 percent of the bilaterian genome entails novel HGs!

But wait, there’s more. Last year a paper was published in eLife titled “The genetic factors of bilaterian evolution.” The paper further affirmed the claim that the origin of animals required many new genes. I covered this paper, too. It reported that 157 new genes were required during the Cambrian explosion to account for the origin of bilaterians. As they wrote:

The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.

Peter Heger et al., “The genetic factors of bilaterian evolution,” eLife, 9 (2020), e45530.

In short, recent papers have spectacularly confirmed Meyer’s position in Darwin’s Doubt, and now in Return of the God Hypothesis. Meyer was aware of this evidence when he wrote his latest book, which is why he wrote on page 318, “I did and still do suspect that much of the genetic information necessary to account for the abrupt appearance of the Cambrian animals arose in the Cambrian period. (Recent genetic analyses have confirmed my view.)” He then documented the sources for these genetic analyses in an endnote in an endnote:

As it happens, recent comparative studies of the genetic diversity of the animal phyla have confirmed my original contention rather than Marshall’s proposal. These studies have established that many thousands of novel genes did arise abruptly during the Cambrian explosion in order to build the first animals. As Jordi Paps and Peter Holland, the authors of one study, put it: “Contrary to the prevailing view, this [study] uncovers an unprecedented increase in the extent of genomic novelty during the origin of the metazoans,” that is, during the period of or just before the appearance of the disparate body plans in the Cambrian explosion (emphasis added). The authors concluded that “internal genomic changes were as important as external factors in the emergence of animals” (“Reconstruction of the Ancestral Metazoan Genome Reveals an Increase in Genomic Novelty”).

(Return of the God Hypothesis, p. 499)

Meyer’s citation here is in fact the same study by Paps and Holland that was cited above, meaning it was entirely appropriate for him to cite the origin of numerous new genes in the Cambrian explosion as a serious problem for neo-Darwinian models of animal evolution, both in his book and in his interview with Peter Robinson.