I’m no longer crushed under the weight of classwork, so I made a video about a creationist who tried to suggest that Eric Davidson’s work on gene regulatory networks somehow conflicted with evolution. Oops. I had to deal with that.

Text below the fold for those of you who hate watching videos.

Hey, friends–

Did you miss me? I’ve been absent for a while, my excuse being that it has been the end of the semester, and I’ve just been buried in the work that pays my salary, so I’ve been slacking on keeping up the channel. Now the semester is almost over, though, and a huge burden has been lifted off my shoulders, and now at last I can relieve an itch that has been bugging me for a few weeks.

You see, I encountered this guy on Twitter, a typical creationist of the pompous species. Their pseudonym is “slave of the lamb,” which already annoys me — its the standard humble brag, pretending that they ar a mere slave to their imaginary god, so that they can then act all superior to those who aren’t wearing their self-imposed and ineffectual chains. Persecution, it’s what these kinds of christians wallow in.

But that’s nothing. Let’s set that aside and look at the substance of what they are saying. This is what really bugged me. They’re trying to create doubt about evolution by appropriating scientific language.

“Random mutation, natural selection, and reproduction aren’t viable mechanisms for the types of changes you need for evolution. We know this because we’ve observed developmental gene regulatory networks in the process of ontogeny and the only viable changes are at the periphery.”

My eyebrows started to rise with the words “developmental gene regulatory networks.” This is a topic I know more than a little about, and I’m already a little peeved at someone claiming that developmental biology is an obstacle to evolution. No, that’s silly. Ask an evo-devo person about that, and they’ll tell you that development and evolution go hand in hand, working together to generate the patterns we see in nature.

Further, though, this is pretentious nonsense. They’re throwing around big sciencey words about concepts they clearly don’t understand to create an illusion of scientific support for their claim. I knew this instantly because I recognized the language they were using, and knew right away that they were cribbing from Eric Davidson, a well-known Evo-Devo guy, and that they were distorting the meaning of an accepted concept in evo-devo circles, one that is not at all contrary to the idea of evolution. I could even guess which specific article they were mangling, a guess that was later confirmed when they cited it while quote-mining from it.

The title of the article they are citing as evidence against evolution is “EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY”.

Yeah, we could stop there, since their intent is clearly contrary to the content of the paper they are citing. This is an article about the evolution of body plans, not how development is any kind of barrier to evolution. It’s technical stuff, with an assumption of knowledge about the deep background of the subject under question and not at all the kind of thing that you can throw into a Twitter conversation…unless your goal is to kill the discussion dead. That’s bad enough, but just a glance at the title should reveal that it is an attempt to mislead.

So now you’re in for it. I’m going to explain what this paper is actually saying.

Let’s jump into the abstract.

“At present several entirely different explanatory approaches compete to illuminate the mechanisms by which animal body plans have evolved.”

Right there. First sentence. Davidson is going to compare mechanisms BY WHICH ANIMAL BODY PLANS HAVE EVOLVED. This is not to argue that animals didn’t evolve, but that there are multiple mechanisms for that fact. He’s going to focus on different levels of explanation.

“Their respective relevance is briefly considered here in the light of modern knowledge of genomes and the regulatory processes by which development is controlled. Just as development is a system property of the regulatory genome, so causal explanation of evolutionary change in developmental process must be considered at a system level.”

What he means here is that it is not sufficient to understand the function and origin of single genes. We have to look at systems involving multiple genes and patterns of interaction between them. As we’ll see in a bit, he’s going to argue against an overly reductionist approach, where evolution can be summarized as a series of tiny shifts in allele frequencies.

“Here I enumerate some mechanistic consequences that follow from the conclusion that evolution of the body plan has occurred by alteration of the structure of developmental gene regulatory networks. The hierarchy and multiple additional design features of these networks act to produce Boolean regulatory state specification functions at upstream phases of development of the body plan. These are created by the logic outputs of network subcircuits, and in modern animals these outputs are impervious to continuous adaptive variation unlike genes operating more peripherally in the network.”

Uh-oh. Do you suddenly find yourself lost in the weeds? I’ll come back to that last sentence in a bit, because that’s clearly where our creationist got the idea about developmental systems being unable to evolve deeply — but in order to understand why they’re not understanding the paper, you need to know what developmental gene regulatory networks are.

To start simply, you know that single genes don’t identify the properties of tissues and organs. There isn’t a “liver gene” that gets switched on to form a liver. Instead, there’s a plethora of molecular signals that impinge on an undifferentiated cell, and those signals trigger a whole complex cascade of activities that lead eventually to the differentiation of a liver cell.

For example, one signal might be the secreted Wnt protein, which binds to the Frizzled receptor in the membrane of a cell. Is Wnt the triggering signal to make a liver, or is it Frizzled? Or is it the interaction between Wnt and Frizzled? We clearly have to step back and look at the process as not one about what a single gene does, but what the combination does. Then further, Frizzled activates a series of proteins, like GSK3 and beta-catenin. So the system we have to examine is Wnt + Frizzled + GSK3 plus a whole lot of other gene products. To make it even more complicated, Wnt doesn’t initiate liver development EXCEPT in combination with many other signals.

The point is that if you want to understand how an organ develops and evolved, it’s not just about how single genes were tweaked by mutation and adaptation over time, but about how a pattern of relationships between genes evolved. Davidson approached this problem by analyzing the gene interactions as circuits, showing that we can map out how genes talk to one another as a kind of circuit diagram, and that’s what he spent most of his career working on. We can visualize the pattern of interactions between genes as lines on a diagram, as in this example.

This is part of the genetic circuitry involved in specifying endoderm and mesoderm in an echinoderm. It shows the relationships between all these genes in forming different tissues, basically how signals are passing to switch on or off the various genes associated with these tissues in a developing sea urchin. It’s comparable to an electronic circuit diagram in that we are not necessarily hung up on the details of how a capacitor or resistor works, but more interested in what is soldered to what.

You might look at that and say it looks like a complicated mess, and how can we extract any utility from this kind of diagram? You’d be right, this is a kind of shorthand, a crude sketch of the relationships of the genes. Where it becomes interesting, though, is that it allows you to compare the circuitry of different organisms and see where they are similar, and where they are different. What he has found is that the way one echinoderm specifies endoderm is the same in other echinoderms. Mostly. There are small differences in different species of echinoderms, but the overall circuit is recognizable and similar.

That’s where Davidson is going with that last sentence of the abstract.

“These are created by the logic outputs of network subcircuits, and in modern animals these outputs are impervious to continuous adaptive variation unlike genes operating more peripherally in the network.”

They examined many different species in the phylum Echinodermata, for instance, and find that there is a common core in the gene circuitry that is conserved. That makes sense. When the ancestor of all modern echinoderms worked out the circuitry to make a gut sometime back in the Cambrian, it was conserved in all of its descendants, because they all required the basic functionality to make a gut. An animal that had a mutation to this core circuit that prevented proper gut formation was a dead animal and would leave no descendants.

A gut is a central part of an animal’s body plan. All he is saying there is that the body plan, this circuit, is more resistant to change than more peripheral features relative to this core. So, for instance, we can tolerate more variations to something like the shape of your nose than we can to changes in whether you have a nose or not.

That’s the gist of what Davidson is saying. Elements of the organism that are dependent on the pattern of interactions between many genes are more resistant to change than details that hinge on a small number of genes. This does not hamper evolution at all: note that echinoderms may make their guts in similar ways, but echinoderms still encompass all the diversity of starfish, brittle stars, sea urchins, sand dollars, sea cucumbers, and sea lilies.

Not everything in Davidson’s work is uncontroversial, which is probably the only thing the creationists cared about. Davidson is rather aggressive in dismissing aspects of old school evolutionary biology, and that’s the bit Slave of the Lamb chooses to quote. Selectively. They leave off this bit.

“Of the first of these approaches (e.g., Hoekstra and Coyne, 2007), I shall have nothing to say, as mechanistic developmental biology has shown that its fundamental concepts are largely irrelevant to the process by which the body plan is formed in ontogeny. ”

Heh. I found that amusing, and accurate. Coyne has been rather fiercely opposed to aspects of evo-devo — he got into quite a few arguments years back over the somewhat esoteric issues of cis-regulatory factors vs. trans acting genes which I won’t get into here. He was on the wrong side of history on this one. This comment from Davidson, though, has a narrower scope. He’s arguing not that mechanistic developmental biology, and the incremental gradualism of Darwinian evolution, are wrong, but that they don’t apply to the issue of body plan evolution. The qualifier of “body plan evolution” is an important one in this paper.

Davidson is arguing that just thinking in terms micro-evolutionary adaptation of single genes is inadequate to explain the evolution of phyla — we need to consider whole circuits and patterns of interactions between genes. He continues:

“Neo-Darwinian evolution is uniformitarian in that it assumes that all process works the same way, so that evolution of enzymes or flower colors can be used as current proxies for study of evolution of the body plan. It erroneously assumes that change in protein coding sequence is the basic cause of change in developmental program; and it erroneously assumes that evolutionary change in body plan morphology occurs by a continuous process. All of these assumptions are basically counterfactual. This cannot be surprising, since the Neo-Darwinian Synthesis from which these ideas stem was a pre-molecular biology concoction focused on population genetics and adaptation natural history, neither of which have any direct mechanistic import for the genomic regulatory systems that drive embryonic development of the body plan.”

Body plan, body plan, body plan. This is all about how patterns of multicellular organization arose back in the pre-Cambrian, and have been maintained for the last half billion years. It is ridiculous to pretend that this work gives any comfort at all to creationist notions, or in any way calls into question the fact of evolution.

What Slave of the Lamb is doing is classic creationist dishonesty and misdirection. They are:

Quote-mining. They finely parse fragments of a paper out of context, approaching it like bad theology: all we have to do is chop at the meaning of individual words until they can claim the whole has their desired interpretation, ignoring the larger sense of the paper.

Misrepresenting. They present their version of the story as if, gasp, the evolutionists have been hiding this dirty little secret of their own disbelief in evolution. This is not the case. Every evolutionary biologist will tell you that there are many mechanisms of evolutionary change. If we say that drift is an important process in evolution, that does not imply that we reject natural selection.

Privileging authority. Religious arguments are ultimately arguments from authority — an invisible phantasmal authority they alone can hear. So they give excessive credulity to citing (often incorrectly) Big Names in biology. I respect Eric Davidson’s work, but I’m not going to drop to my knees and automatically praise his ideas when a creationist name-drops him. Especially when they clearly do not understand him.

Dressing up in a lab coat. Years ago, I had a good laugh at a “documentary” put on by the televangelist D. James Kennedy, who was going to prove evolution was wrong. The show opened with Kennedy in a lab coat, in front of a table full of bubbling flasks and beakers full of colored water. This is the same thing! See? I can quote a peer-reviewed paper from the scientific literature, and use scientific jargon, so I must be smart. Sure, Otto, you just don’t understand it.

Well, there. I have scratched my itch, and I hope you might have learned a few things. I can honestly recommend the work of Eric H. Davidson if you want to dig deeply into how genes are regulated in development and evolution. Unfortunately, he died in 2015, but I’ll read a bit from his obituary in PNAS.

“Eric H. Davidson, a world leader in developmental biology, demonstrated that most of development is, indeed, regulated by the genome. He was a pioneer researcher and theorist of the gene regulatory networks that execute the most complex biological processes, such as the cascade of molecular mechanisms that transform a single-celled egg into a complex creature. He insisted that the seemingly infinite details of classical developmental biology had to be explained in terms of the function of DNA sequences inherited in the genome, and showed how genomic information is used to initiate and drive forward development.”

Right. And this is the guy a creationist chose to misinterpret to cast doubt on evolution, the scientist whose last book was titled “Genomic Control Process: Development and Evolution”.