Pharyngula

Paul Nelson has deigned to write a two-part essay on “Ontogenetic Depth“, his sciencey made-up term for a metric that he claims makes evolution essentially impossible. We’ve been wrangling over this for a long time — he and Marcus Ross introduced this in a poster at the Developmental Biology meetings in 2004, titled “Understanding the Cambrian Explosion by Estimating Ontogenetic Depth”, and in our conversation at that time I certainly got the impression that he and Ross were busy collecting this peculiar thing alien to creationists called “data”. I have asked him multiple times over the last 7 years how to estimate this hypothetical number; at the meetings, I recall asking him specifically how I would go back into my lab and measure it in my zebrafish. He was evasive. We’ve been trying to get him to explain this datum, which was his pretext for getting into a professional meeting, and gotten nothing.

Well, now we’re done. His first point in his first essay is that “ontogenetic depth” is “A Biological Distance That’s Currently Impossible to Measure”.

Oh.

So what the heck were Paul Nelson and Marcus Ross doing? Nelson was certainly doing his best to pretend that they were actually doing real work on this metric, but I should have known better: a failed young-earth creationist philosopher could not possibly have been soiling his hands with empiricism. Now he’s frantically arguing that it doesn’t matter, that once upon a time no one knew the distance from the earth and the sun, but they could at least name the concept, so he can take credit for at least recognizing a real problem, and he can also patronizingly thank me for pointing out that they don’t actually have the tools right now to actually measure it.

Wait, how can they thank me for that? I’m picturing Nelson and Ross sitting at a microscope and looking at eggs of a nematode or a zebrafish or a frog, rubbing their hands in anticipation of a productive morning, and then staring at each other and wondering what to do next…and end up inventing a term for something that they don’t know how to measure. And then a year or so later, Nelson encounters me, I peevishly tell him that he doesn’t know how to measure cell division and differentiation in terms of a single numeric metric, and seven years after that, Nelson finally slaps his forehead and admits “Hey, we don’t know how to measure that!”

I don’t want credit for pointing out the obvious to the clueless, especially not when they’re that slow.

His first essay is an exercise in rationalizing away how he could propose this obstacle to evolution while not having the slightest idea how to measure it. His second essay is an exercise in demonstrating that he doesn’t understand basic biology. He has gussied it up with brightly colored diagrams of cell pedigrees that he purports illustrate the problem, but I think are actually more intended to distract and confuse and make you think he’s actually thought deeply about the subject.

Here’s the gist of his conceptual difficulty: he can’t imagine how the first metazoan got from a crude colonial state, where it’s just a mass of identical cells clumped together, to a state in which regions are consistently specialized for specific functional roles, with the simplest example of an animal that contains only two cell types, a mass of somatic cells that take care of feeding and motility, and a smaller mass of germ cells that do the job of reproduction. Why, that would require a whole series of mutations that selection can’t possibly explain! How could selection possibly create a cell that contains a series of instructions to build a cell type that isn’t going to reproduce?

I’m wishing that Nelson hadn’t chosen to focus on biology. If only he were a creationist philosopher of physics, he’d be the one asking, “magnets, how do they work?” and somebody else would get the job of correcting him.

Nelson summarizes the problem as, at the minimum in the simplest possible metazoan, a three step sequence. First, cells have to divide and stick together; second, they have to have a way to make daughter cells differ from one another; and third, there has to be inheritance of that differentiated state in sublineages. He claims that in none of these steps can selection be involved; this complex process had to evolve independently of any selective effects.

That’s nonsense. The first metazoan already had all the tools needed to build these steps, honed by a billion years or more of selection in single-celled organisms. All three of his steps are found in bacteria.

Step one is simply cell adhesion. Step two is gene regulation. Step three is epigenetics. That’s it. These aren’t glorious novelties invented by the first animals, they inherited this toolkit from their ancestors. Bacteria have been sticking together for billions of years, and they’ve been responding to their local environment by shifting patterns of gene expression for just as long. A bacterium in a sugar-rich environment vs. a bacterium in a sugar-poor environment will make long term changes in gene activity that can persist for a few generations using exactly the same mechanisms as an animal embryo sets up germ and somatic tissues; has Nelson never heard of Jacob and Monod?

Nelson’s argument goes beyond pure ignorance, however. He also recruits Lewis Wolpert to his side, which is remarkable. Wolpert is a brilliant and influential developmental biologist who shaped many of our ideas about differentiation, pattern formation, and evolution. He cites Wolpert as postulating as serious problems for evolution the origin of the egg, and in particular implying that Wolpert sees metazoan evolution as violating a principle. Here’s what Nelson says about a particular paper Wolpert wrote.

Evolutionary developmental biologist Lewis Wolpert — whom no one, even in his wildest delirium, would ever mistake for an ID theorist — had long critiqued the scenario on functional grounds, using what he called “the continuity principle.” (1994) The continuity principle requires that any change occurring in an evolutionary transformation be biologically possible, that is, viable and stably heritable in the next generation.

Whoa — eminent anti-creationist scientist critiques an evolutionary explanation! I’m sure this must make you wonder, familiar as you are with creationist tactics, what Wolpert actually said. Judge for yourself, here’s the abstract for Wolpert’s paper, does it sound like he’s on Nelson’s side at all?

A scenario for the evolution of a simple spherical multicellular organism from a single eukaryotic cell is proposed. Its evolution is based on environmentally induced alterations in the cell cycle, which then, by the Baldwin effect, become autonomous. Further patterning of this primitive organism–a Blastaea, could again involve environmentally induced signals like contact with the substratum, which could then become autonomous, by, perhaps, cytoplasmic localization and asymmetric cell division. Generating differences between cells based on positional information is probably very primitive, and is well conserved; its relation to asymmetric cell division is still unclear. Differentiation of new cell types can arise from non equivalence and gene duplication. Periodicity also evolved very early on. The origin of gastrulation may be related to mechanisms of feeding. The embryo may be evolutionarily privileged and this may facilitate the evolution of novel forms. Larvae are secondarily derived and direct development is the primitive condition as required by the continuity principle.

This is a paper in which Wolpert explains how multicellularity could have evolved, directly answering the questions Nelson raised with his supposedly problematic three steps. How did Paul Nelson miss that?

But wait! There’s more Wolpert abuse!

Nelson has found a paper by Wolpert in which he points out a serious problem in a particular evolutionary strategy, and Nelson, apparently primed by a selective reading of science papers for the magic words “problem”, “difficulty”, “impossible”, or “unlikely” has seized upon it as another instance of Eminent Scientist Critiquing Evolution.

What mechanism is coordinating gene expression among all the members of the colony, such that only one cell lineage will evolve to carry the complete instruction set required to specify the form of the whole? How are mutations — occurring in all individual cells of the colony — transmitted to the next generation? If individual cells continue to reproduce via normal fission, or budding, notes Wolpert, “cell lineages [will be] mutating in all sorts of directions in genetic space.” (2002, 745) Given such genetic chaos, he argues, “we consider it practically impossible” for the collection of cells to “yet retain the ability to evolve into viable new forms.”

Sounds dreadful. I give up, I guess evolution must actually be impossible.

Hang on, though, maybe we should read Wolpert’s paper first. And there what you discover is a story that you would not have expected from Nelson’s peculiarly distorted coverage. It’s a short paper where the authors consider alternative reproduction strategies: not all animals go through a single-cell stage in reproduction, you know. Some, like hydra, reproduce by budding, where a small collection of cells, not just one egg or sperm cell, splits off to form an independent organism. Wolpert is considering which solution is more advantageous for evolution, going through a single-cell bottleneck or through a larger population that would reduce the dangers of mutations? And that’s where Wolpert’s criticisms lie: the asexual budding solution is the focus of his critique, and which is where Nelson draws his quotes highlighting the difficulty of evolution.

In a hydra-like organism that only reproduces by asexual budding, it is impossible to evolve significant changes. There is no way that the genes in the huge number of cells involved in budding can change at the same time, and mutations in individual cells mean that they no longer share the behavioural rules of the majority. It is only through a coherent developmental programme, with all cells possessing the same genes, that organisms can evolve, and this requires an egg.

Huh. So Wolpert is arguing that development from a multicellular propagule is much less evolutionarily flexible than evolution from a single-celled egg. His thesis is explaining why we develop from eggs, not that our evolution is unlikely.

We consider it practically impossible to have many asexual, differentiated cell lineages mutating in all sorts of directions in genetic space and yet retain the ability to evolve into viable new forms. This may not be completely impossible but, taking the broad view in evolutionary terms, organisms that develop from an egg would displace those that do not.

Dang, Paul Nelson. You should be smart enough to know that you don’t quotemine claims from the science literature in an argument with someone who has actually read that literature.