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for a number of reasons. The mistakes that have been made are not mistakes of bad science, but of interpretting things incorrectly based on limitted data.
There are a number of things that are now becoming clear as we move into the 21st century that were not at all clear just 30 years ago, such as:
1) All animal life has a discoverable evolutionary history, and a single 'real' tree can be discovered, and is being discovered. This 'real' tree is somewhat different from the 'trees' that have been proposed prior to the advent of genetic analysis and morphological cladistic analysis. This 'real' tree (and I put real in quotes because it's as real as can be discovered without the aid of time machines) has a number of early, 'primitive' groups branching off very early, the first branch being sponges, the next cnidarians (corals, anemones, and jellyfish), the next ctenophorans (comb jellies). The animal groups that are left comprise a clade known as Bilateria, which refers to (surprise!) bilateral symetry. All modern bilaterians are in one of two groups: Deuterostomata or Protostomata.
Deuterostomes are composed of echinoderms (starfish, urchins, seacucumbers, crinoids, and a number of other weird extinct things) and chordates (which include vertebrates, as well as amphioxus, sea squirts, and graptolites). Deuterostomes may seen like a weird group, but there are a lot of embryonic, developmental, and fossil links between the two major, modern clades.
Protostomes comprise everything else, and are also composed of two major groups, the Lophotrochozoa and the Ecdysozoa. Lophotrochozoans have either an eversible proboscis or lophophore and include molluscs, annelids, deep-sea tube worms, brachiopods (or lamp shells), bryozoans (moss animals), and flat worms. The ecdysozoans are comprised of animals that molt their skin (a process known as ecdysis), and include arthropods, tardigradans, onychophorans (modern velvet worms as well as fossil stuff like Hallucigenia), and some other worms like nematodes and nemertians.
Gould's writing, especially in Wonderful Life, seems to minimize the importance of this (at least to me). He talks about diversity vs disparity and the cone of diversity etc, and totally misses what I think is the point: weird stuff is weird, but it's not so weird that its evolutionary history becomes unknowable. Jeffrey Levinton called this kind of thinking "the evolutionary lawn" approach, as opposed to an evolutionary tree, and I agree with him. By overstating the weird and ignoring the shared features, you overpopulate the Cambrian and overstate the case for a Cambrian explosion.
I also see a parallel between this kind of thinking in evolutionary biology, and the thinking I see in linguistics that the linguistic heritage of some languages will never be known. I think the problems with linguistics may be harder than they are with evolutionary biology, but to say that for instance Basque or Zuni are just too unique to ever know what they're related to is, to me, a silly way to go about science.
2) Taphonomic mode is absolutely the most important thing to be thinking about when looking at fossils of Cambrian or earlier age. For some background, taphonomy is literally the study of burial, and is used by both paleontologists and archaeologists. A taphonomic mode is a somewhat unique way of preservation. Most fossils found in near-shore to off-shore shelf environments are preserved by the same taphonomic mode: hard parts preserved in sand, silt, or lime mud. Ocassionally, there are laggerstatten--sites with fantastic preservation for unusual circumstances--where stuff like soft bodied organisms or soft parts of organisms with hard skeletons are preserved. For example, the feathered dinosaurs in China are found in a laggerstatte.
But, every fossil site of Cambrian age or earlier, was preserved by a "unique" taphonomic mode that became "extinct." The Ediacaran faunae represent soft bodied organisms and were found preserved in medium grained sandstones. The Burgess Shale and related faunae were found in muds, and preserve soft parts in three dimensional detail. This kind of preservation is almost entirely unknown after the Cambrian.
What makes the Cambrian and earlier fossils so cool (and important) is the lack of something called vertical bioturbation. Bioturbation is sediment being disturbed by burrowing animals. No animal built a burrow deeper than 1.0 cm until the Ordivician. This is especially important in the Ediacaran, as the lack of bioturbation allowed bacteria to form very thick, very solid, microbial mats on the surface of sandy beaches in the subtidal zone. Instead of loose sand, these sandy areas were semi-solid gelatenous platforms. When a storm brought in a new influx of sand or mud, this new sand or mud burried the unfortunate organisms and forced them to make an imprint in the gelatenous substrate; actually a lot like a footprint. The lack of bioturbators also prevented these imprints from being destroys.
Because the taphonomic mode of the Ediacaran faunae was so muddied and unclear until recently, people were interpretting the Ediacaran organisms as weird body fossils. This is an incorrect interpretation, as they're really much more like full body trace fossils. Where people previously lamented the lack of GI-tract in Ediacaran fossils, they now realize they shouldn't see them at all.
3) The rock record is more incomplete the farther back in time you go. This isn't actually a new development, but the extent of pre-Burgess Shale incompleteness wasn't realized until fairly recently. Between Ediacaran-type faunae and Burgess-type faunae, a worldwide unconformity exists. This, as well as the assumption that Ediacaran fossils were something weird, makes the Burgess Shale look look sudden and bizzar. Also, prior to the Ediacaran faunae, a tremendous ice-house period existed. The possible only equatorial rocks from that time are a little inaccessable now, as they're high in the Pamirs and Zagros, and most likely deformed or long-since subducted.
SO..... If we look again at what happened before and during the Cambrian explosion, we see something a little different than what Gould wants us to see. Most Ediacaran fossils look a lot like what you'd imagine early animals would look like. Many are very similar to sea pens (colonial cnidarians), and many others look like they belong to to the deuterostome, echinoderm, ecdysozoan, and molluscan clades. Because we now know the fossils are preserving just the outside of the organisms, there's no reason to propose new, unique, and extinct organismal groups for them, and it becomes clear that animals were diverse and plentiful a long time before the Cambrian explosion.
There are some Ediacaran fossils which are genuinely weird and don't at first glance belong to any modern groups (such as Dickinsonia, Pteridinium, and Tribrachidium). This doesn't mean they really were something weird and unique in Gould's sense, but in my opinion, probably belong to stems of groups such as Bilateria.
There are two things that happened however between Ediacaran time and Burgess Shale time: macropredation first evolved, and hard part first evolved (probably as a response to predation). That's it.
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