Early mutations and new body plans

A claim I see made by a lot of ID proponents, especially Steve Meyer, is that evolution can’t create new body plans because the mutations that are needed to do that are early in development and mutations that are early in development are lethal. The argument goes something like this:

“ Molecular biology presents an even greater conundrum for evolutionists, he noted. Any genetic mutation capable of creating a new life form would need to alter a gene that acts early in the organism’s development and controls the expression of other genes that come into play later on. But mutations on early, developmental genes kill an organism long before it can reproduce.“

You also see this paper referenced frequently:

“As an example, Gelernter cited the work of German geneticists and 1995 Nobel Prize winners Christiane Nüsslein-Volhard and Eric Wieschaus. The scientists attempted to induce macroevolution in fruit flies by introducing every genetic mutation they could think of. But every mutation they tried turned out to be a dead end, killing the fly long before it could mate.”

Now to me, this just doesn’t seem like an issue. I think its safe to say that early mutations in development weren’t as inflexible back around the Cambrian. Surely a few hundred million years of building around a certain way of doing things will do that to a lineage.

But I would love to hear those more informed than I give their thoughts

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This is known as the “loose genes” theory. Or it was when we discussed it in Dave Jablonski’s macro seminar 25 years ago.

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As I understand the issue, these genes can be thought of as the foundation of a building. When the foundation is being built, it can be almost any shape. But once a structure is built upon it, even minor changes to the foundation can bring the whole thing crashing down.

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@Art @Rumraket @Mercer @davecarlson @evograd @glipsnort I would love to hear all of your thoughts on this argument of theirs as well.

So, if mutations in “early, developmental genes kill an organism” and are somehow incompatible with both life and evolution, then are polymorphisms in, say Hox and homeotic genes impossible? Anyone want to guess?

Ooh, also, can anyone think of a way that mutations in body-plan genes can happen without causing catastrophic morphogenetic failure or other major phenotypic train wrecks? Oh look!

https://www.cell.com/current-biology/fulltext/S0960-9822(19)30688-8

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I would also point out that small changes to transcription factor binding sites (or evolution of new, weak sites) can incrementally affect expression and thus incrementally affect phenotype. Gradualism!

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To quote the eminent Tim Blais:

Adult and embryo mostly don’t evolve in the genes of the genome. Safer the mutation aimed at regulation, keep the building blocks and swap their activation.

It’s not surprising that protein-coding mutations to key developmental genes (as Nüsslein-Volard and Wieschaus did) would be overwhelmingly detrimental. But sure, let’s pretend that this comment from Wieschaus in 1982 is the final word on evo-devo:

The problem is, we think we’ve hit all the genes required to specify the body plan of Drosophila, and yet these results are obviously not promising as raw materials for macroevolution. The next question then, I guess, is what are - or what would be - the right mutations for major evolutionary change? And we don’t know the answer to that.

I think that’s basically right, we see the same thing with novel genes, with the genetic code, and with metabolic pathways. In the beginning they’re usually just beneficial, perhaps even strongly so. But over time as additional steps in a pathway, and new interactions between other genes build up around them they become fundamental to many other processes and lose their flexibility.

This is just how it works. To truly recreate the macroevolutionary steps that led to some body plan, a lot of other pathways and genes that today interact with these fundamental developmental genes need to be either changed to their ancestral state too, or deleted entirely because they simply didn’t exist back then.

The same issue also explains how the genetic code has become largely “frozen”. When new amino acids were added to the code they might have only seen use in a single or a few codons in the entire proteome of an organism. But as an increasingly greater proportion changed to include the new amino acid, it’s loss would eventually become lethal.

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Out of context, that seems a trivially easy question to answer: Macroevolutionary changes now occur at levels above that of basic body plan, such as how the basic vertebrate body plan has diversified into the many forms it has taken over the past 500 million years. Am I missing something?

So what organisms did fruit flies evolve from anyway, how did they look, and which genes determine fruit fly morphology to be different from their ancestor? I’m guessing another very similar fly. When did the “body plan” of flies get established, and what was the ancestor of all flies even like? Another similar flying insect? I think we’d have to go really far back to get at the basic insect body plan way before the origin of flies.

Since John Harshman mentioned David Jablonski, I should point out that the latter continues to work on this question (i.e., non-uniformitarian modes of evolutionary innovation in the animals, in relation to the hierarchical structure of their developmental gene regulatory networks [dGRNs]). This 2017 paper and its second part are open access:

Under the section heading, “Origin of Novelties in Time and Space: Empirical Challenge for Theory,” Jablonski writes:

The Cambrian explosion of animal body plans, and, not coincidentally, the first appearance of most phylum-level taxa, is unmatched in the preceding 4 billion years or the ensuing half-billion (see Erwin and Valentine 2013 and Erwin 2015a on the uniqueness of this event). This geologically brief interval when virtually all fossilizable bilaterian body plans appeared for the first time is perhaps of greatest interest in terms of (a) how eukaryotic development as constructed in the Proterozoic—presumably derived though some combination of stepwise selective modification and frozen accident—has both promoted and limited evolutionary change ever since, and (b) whether phenotypic evolution in the late Proterozoic and the Early Cambrian represent a mode of evolution inaccessible to later genomes, populations and clades, or a unique ecological situation.

Earlier in the same paper, Jablonski addresses what he calls the “semi-hierarchical” nature of dGRNS, and the consequences for macroevolutionary transitions:

This structure is widely held to affect the probability of different transitions, although the specifics are not sufficiently understood to ground a robust theory: some alterations are more readily achieved than others, in part owing to the higher or lower position of different regulatory nodes within a network, but also via connections to preexisting and novel circuits near the network periphery (Davidson and Erwin 2009; Payne and Wagner 2013:; Rebeiz et al. 2015). Thus the probability distribution of the raw material for evolution in a genotype or phenotype space—the inputs presented to selection and other sorting processes—is not isotropic, but uneven, skewed, or channeled. This probabilistic approach to developmental constraint, with some evolutionary directions absolutely unavailable and others accessible to varying degrees (Maynard Smith et al. 1985; Schwenk and Wagner 2004; Klingenberg 2005; Hallgrímsson et al. 2009, 2012; Gerber 2014), may enable stronger mechanistic connections between development and differences in clade behavior in morphospace (Salazar-Ciudad and Jernvall 2010; Gerber 2014 and references therein). That said, we know little about which developmental differences tend to give rise to macroevolutionary ones.

As is customary for Jablonski – thorough and thoughtful scholarship. Both parts 1 and 2 of this major review provide an excellent introduction to the relevant literature.

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For me the most amazing thing is the difference between human and mouse early embryogenesis:

This, to me, shows that the foundation is incredibly robust and can withstand a lot of evolutionary tinkering.

I’ve noticed that most evolution denialists have a mental model of development that requires a set of different genes to build a different structure. Nothing could be further from the truth.

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Body plans of the Cambrian are not what the typical ID enthusiast think they are. They seem to be of the impression that humans, mammals, fish, birds, reptiles, and amphibians are separate body plans (as per the Cambrian usage of the term). And within each class are further examples of body plans, like frogs, turtles, snakes, newts, etc.

ID theorists never seem to clarify matters for their supporters, that all these examples belong to one Phyla, chordata (vertebrata).

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Exactly. A new organelle is more amazing than a new body plan.

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What exactly is a “body plan?”

Are you asking because you don’t know, or is the word “exactly” a statement? I suspect the latter.

I have yet to have a clear definition of what a “body plan” could be. For example, do whales and humans have the same “body plan”? It seems that they do.

Yes, they do. But if you want a “clear definition” then this will become an uninteresting semantic pub crawl. If you are actually curious about body plans, there are lots of interesting papers about them from various angles. I recently read this one, and just found this paragraph that I think probably encapsulates both the uncertainty and the “truth” that is captured by phyla and their associated body plans.

While this multitude of ideas shows a profound lack of consensus, some aspects of phylogeny and character evolution seem, nevertheless, to have been accepted. Most significant is the accurate and, for the most part, unchallenged grouping of species into phyla, such as chordates, molluscs, annelid worms or arthropods, whatever the subsequent discussion of between-phylum and within-phylum relationships. A phylum is the most inclusive classificatory subdivision within the animal kingdom. Phyla (like all clades) are characterised by a set of diagnostic characters unique to the group — notochord and dorsal nerve chord for chordates, shell, radula and muscular foot in molluscs. To an extent, the designation of a phylum is an admission of ignorance regarding these higher-level relationships: the body plan defining a phylum is well defined but relationships to groups with other body plans are less clear.

https://www.cell.com/current-biology/fulltext/S0960-9822(15)00928-8

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I suspect the reason that the term “body plan” comes up so much is because:

  1. It evokes a certain meaning in public communication.
  2. This evoked meaning is quite different than any technical sense of the term.
  3. There isn’t a sharp technical meaning of the word.

So, when we talk about the Cambrian Explosion being the “sudden” origin of all “body plans”, the image this evokes in the public diverges substantially from what the evidence actually shows. For example, I am sure that most the public would think whales and humans have different body plans, but the CE didn’t give rise to a whale body plan distinct from a human body plan.

I’m sure the term has some utility, but there also seems to be a lot of confusion here in how it is communicated to the public. Intentionally or not, some seem to be taking advantage of that confusion.

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Technically, it is a misnomer.

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