That is surprisingly combative. I’m not blaming language. Scientists can and should use the term as they see fit. I’m just pointing out that the term seems to be exploited to sow confusion.
As for the version of Christianity that sows this confusion? I’m not anti-evolution. I’m not part of that version of Christianity. I am also doing my part to clean up the mess. But you already know this.
Every term in biology can be exploited to sow confusion, and this one, “body plan,” is not notably more well-suited to religious dishonesty than others.
Is that a different god? Is it one of the sleeping gods?
You don’t see moral complacency in turning a discussion of “early mutations and new body plans,” which is full of interesting unanswered questions, into an exploration of how phrases can be abused by dishonest religionists? At the least, don’t you think you should own the fact that your religion is the one sowing confusion?
I’m not going to hide my frustration with the ongoing epic failure of Christians to ask why it is that their religion is causing so much harm.
I really wanted the argument that evolution needs early mutations for significant evolutionary change to happen but early mutations are lethal to be addressed. Perhaps the body plan discussion should be split into another thread?
I think the claim “early mutations are lethal” is known to be false; more precisely, we know that it is much too simplistic. And “evolution needs early mutations for significant evolutionary change” also seems inaccurate to me, not because we know the opposite to be true but because “early mutations” is just too simplistic. I sense this is not helpful, but maybe it gets us back into an interesting discussion?
I have an intensive research week coming up (starting tomorrow) with Ann Gauger, so I should not commit any time to further discussion in this thread. But it’s Sunday morning, the Sabbath was made for us, so I’ll make a couple of comments here, and encourage you to contact me via email (firstname.lastname@example.org) if you want additional resources.
The mouse / human embryological contrast, provided by John Mercer above, suggests one line of reasoning to follow about early-acting mutations to animal developmental pathways:
Common descent (of the mammals [Mercer’s example], vertebrates, chordates, Metazoa, Eukarya) is the case.
Therefore observed differences in animal development and body plans have arisen via macroevolutionary processes.
Research problem: figure out what those macroevolutionary processes are. They occurred, because (1) and (2).
One of my PhD committee members, Leigh Van Valen, and I talked about this a lot. Reviewing Keith Stewart Thomson’s argument that (1) and (2) obtained, so let’s get cracking on solving (3), Van Valen wrote:
One heretical conclusion which Thomson comes to must, I think, be accepted. This is that evolution occurs at all stages of development, often at early stages of programs leading to the adult. His most conclusive argument for this reminded me a bit of Descartes: Early development does often change; therefore it can…At least such evolution can no longer be rationally dismissed as Goldschmidt’s folly. 
But one can go another direction from the data:
We have no experimental evidence, from any well-studied model system of evo-devo, that animal embryos tolerate early-acting mutations to body plan-affecting regulatory elements (the exception that proves the rule: losses of structures: wings, eyes, etc.). As Jeffrey Levinton, no friend of ID, explained in his monster-size Cambridge U Press monograph on macroevolution:
As a general rule, major developmental mutants give a picture of hopeless monsters, rather than hopeful change. Epigenetic and genetic pleiotropy both impart great burden to any major developmental perturbation…The cyclops mutant of Artemia is lethal. The homeotic mutants of Drosophila melanogaster suffer similar fates…But any geneticist interested in major developmental mutants would be delighted to find viable hopeful monsters in the laboratory, given the various tricks usually necessary to keep developmental mutants in laboratory cultures. But, alas, major developmental mutants are invariably sickly and show pervasive deformities. From both theoretical and empirical points of view, hopeful monsters have led only to hopeless mooting. 
Therefore observed differences in development and body plans may indicate very deep discontinuities in the history of the animals.
Maybe evolutionary processes were quite different in the past, in modes of action that we have great difficulty reconstructing today.
This is the direction that the late Eric Davidson, his frequent paleontological collaborator Douglas Erwin, and many others (particularly in the “extended synthesis” community) have taken. The ID inference drawn by Steve Meyer, as articulated for instance in his book Darwin’s Doubt, parts company on (3). Steve argues that there’s no observational reason for supposing that evolutionary processes were fundamentally different in the past, unless one is a priori committed to common descent, (1), which Steve is not.
Side note to Josh and Steve Matheson: in 1994, at a big meeting at Indiana University on the origin of animal body plans, organized by Rudy Raff (who died recently, sad to say), a raging controversy broke out on the last day of the meeting about the definition of “body plan.” Someone – I can’t remember who, might have been Stefan Bengtson – challenged the attendees to go look up the anatomical diversity within Mollusca:
As I recall, the speaker did this in a semi-joking way: sort of “Don’t worry about this, we all know Mollusca is a bonafide phylum…but you should worry about this! Mollusca is a bonafide phylum, dammit!”
L. Van Valen, "A morphogenetic basis for macroevolution,” Evolutionary Theory 9 (1988): p. 329.
Jeffrey Levinton, Genetics, Paleontology, and Macroevolution (Cambridge: Cambridge University Press, 1988), pp. 252, 254.
Obviously they can tolerate a range of mutations, but what you seem to be asking for is for them to tolerate mutations to these elements that actually radically change the body plan as a result. Of course, radical changes in body plan as the result of isolated mutations are bound to be lethal the vast majority of the time. As the paper @sfmatheson linked earlier suggests, it’s likely that a series of much more subtle mutations that eventually alter the gene regulatory network are better candidates for body plan evolution:
Another thing that is confusing: Would what we call a difference in “body plan” now be considered a difference in “body plan” 500 million years ago, or whenever these “plans” were just developing? Or would they have just been variations of the sort we now observe between, say, different species of ducks? I somehow doubt that, if some extraterrestrial biologists (with extraordinarily long lifespans) had been observing the evolution of life on earth, they would have been thinking, “OK, nice little change there, some good microevolution happening over there. HOLY JUMPING! LOOK AT THAT! A NEW BODY PLAN! THAT CRITTER JUST CREATED A WHOLE NEW PHYLUM!”
It’s a great question. My opinion/impression is that nearly all evolutionary change is “gradual” enough that big transitions and branchings are only evident to mere mortals in retrospect. And yet there is no obvious “gradual” way to add segments to a body plan, to take what seems the best example of an integral (vs continuous) morphological change that can yield an altered body plan. So, while the recent paper on Hox genes that I posted above suggests that even significant morphological changes can occur gradually and experience buffering, there are at least some aspects of body plan architecture that can change in an instant.
At the phylum level, where “body plans” are most clearly divergent and distinguishable, some of the morphogenetic processes are as basic as early developmental cleavage patterns, and changes at that level may have been instantly distinguishable. I don’t know. It’s an interesting question.
They would have been distinguishable, perhaps. Just as a dog bred with a different coloured coat that had never before been seen in the breed would be easily distinguishable. But would it be obvious that this was a change that heralded what would one day be seen as a completely separate phylum?
Yeah, I think it’s a lot worse than that. All of Nelson’s comments and quotes are based on conclusions drawn from “major developmental mutations” examined in the 1970s and 1980s which are, I suspect, overwhelmingly nulls. This conversation is based on comments above, quoted I think from a new book by the DI, about the Heidelberg screen by Wieschaus and Nüsslein-Volhard. This screen was specifically looking for lethal mutants: those that were not embryonic lethal were excluded from the screen. Amazingly, someone is quoted in this thread writing that “The scientists attempted to induce macroevolution in fruit flies by introducing every genetic mutation they could think of.” If that is a reference to the Heidelberg screen, then it’s a falsehood of the kind that can’t be explained by mere error.
I agree. So when we see apparently minor changes occurring today, how do we know these will not, in fact, be changes just as significant as those that led to new “body plans”? That is to say, those who are looking for where the equivalent mutations mght be occurring may well be looking in the entirely wrong places.