v1.2.2 / chapter 9 of 28 / 01 aug 08 / greg goebel / public domain
* Having surveyed the history of the evolutionary idea itself, it is useful to examine one of the major components of evidence in support of it: the evolution of life through the history of the Earth. This chapter provides background on taxonomy, fossils, and the broad geological history of the Earth.
* We share this planet with an astonishing array of other organisms. Even cataloguing all of them is a monster job. The cataloguing scheme that we use today was, as mentioned previously, basically invented by Linnaeus in the 18th century, and hierarchically broke life down into various levels of groupings, starting with "kingdoms", such as the plant and animal kingdoms; then down into "phyla", such as the phylum of vertebrates, including the fish, reptiles, mammals, and other creatures with backbones; then "classes", such as the warm-blooded furry mammals; "orders", such as the carnivores, including cats, wolves, bears, and so on; "genus", such as the cats; and finally the "species", though there could also be races (breeds, variants) of a species.
Ever since Linnaeus there has been debate over how particular organisms should fit into this cataloguing system. Here the assumption is that there are six kingdoms of life. This is just to simplify the discussion, since professional taxonomists -- the group of biologists who worry about the classifications of life forms -- recognize much more than six, though they are not in any agreement over the exact number. Taxonomists, in fact, are traditionally regarded as extremely quarrelsome, Stephen Jay Gould once describing their style of discussion as "names and nastiness".
There is some reason for this, because classification of anything can be difficult -- anybody can see that it can be troublesome to figure out a rational scheme of organizing a large collection of photographs or the like. To be sure, the branching tree of life means that the familial relationships among organisms are not at all arbitrary: of all conceivable relationships, only one can really be right. The problem is figuring out exactly which among the possible relationships is the right one. Clearly unrelated species can sometimes look surprisingly alike -- sharks and dolphins are a good example, though taxonomists haven't had any trouble recognizing them as unrelated for a long time. On the flip side, sometimes related species can look very different -- whales and hippos being the prime example.
There's also the difficulty of distinguishing closely related organisms as separate species: dogs and cats are unarguably separate species, they couldn't interbreed if they tried, but what about cats and wildcats? Some types of wildcats clearly resemble housecats; are they a separate species? What about more distinctive types of wildcats, such as lynxes and caracals? In borderline cases, that is a matter of opinion. The notion of a "species" is a bit misleading, since it's easy to think in terms of a "model number" of a machine, a "Mark I" or "Mark II" or whatever. Models of machines are distinct; not so for closely related organisms.
In the beginning of proper taxonomy, the only real tool taxonomists had was homologies, the resemblances between different species of external and in particular internal biostructures. This was workable to an extent, but homologies could also prove misleading, as noted above. In Darwin's time, the analysis of embryos provided another useful tool, though again one that could be misleading. Determining the correct taxonomic relationship between species requires the integration of multiple aspects of organisms -- and the more aspects, the better.
In modern times, analysis of protein structures has provided an excellent tool for understanding relationships between species. One of the most popular proteins for taxonomic work is "cytochrome c", a component of the cellular energy production system in animals, plants, and fungi that consists of about a hundred amino acids. It is useful because it covers such a range of species. Assessing the similarities and differences between the cytochrome c proteins of different species gives an index of their relatedness. A variety of genetic analysis tools are also now available -- they are discussed later -- that have given taxonomists a big leg up, handed them a few big surprises, and resolved a good number of long-standing disputes. They still bicker, but it's generally over subtler distinctions.
* Modern taxonomy is based on the concept of the "clade". The notion was introduced by the German entomologist Willi Hennig (1913:1976) in the 1950s, though it didn't really hit the scientific mainstream until the 1970s.
A clade is a strict form of family grouping, defining a hierarchy of an particular type and all of its variants. This looks very much like traditional taxonomy in some respects, but it differs in others. For example, in traditional taxonomy reptiles and birds were separate classes, but under cladistics birds had to be included among the reptiles. As defined under traditional taxonomy, reptiles were not a clade, since birds are derived from them, meaning some of the family members had been excluded. By the old definition, reptiles were "paraphyletic", meaning they didn't make up a complete "monophyletic" clade. The definition of reptiles has been considerably adjusted in recent times to conform to cladistic requirements, a matter also discussed in more and somewhat confusing detail later.
Sometimes such paraphyletic groupings are called "grades" instead of clades, if just for convenience since it's identifying a "family" with a large chunk of the actual members thrown out. In the vaguest case, a grade is nothing more than a "polyphyletic" grab-bag of organisms with some specific features in common and with no strong relationships between them. That's Hennig invented "cladistics" in the first place, to ensure that taxonomists understood true relationships and weren't just cataloguing species by some arbitrary and possibly prejudiced scheme of convenience that didn't necessarily reflect the actual relationships. There's nothing wrong with convenience, of course, and grades are still used in taxonomic literature, though there is a push to designate them by attaching a "*" to the name.
Clades also do not by themselves define levels of hierarchy as do traditional Linnaean taxonomic designations. Mammals by themselves form a clade; carnivores form a subordinate clade; the various cat species form a clade beneath that. In addition, clade diagrams or "cladograms" are not "evolutionary trees" as such: they provide a branching tree terminating in offshoots, living and extinct, along branches of variations that don't feature any species themselves, though they may have labels giving the name of the clade defined by particular branches.
In fact, strictly speaking, clades are only defined by taxonomic features, not by supposed ancestry -- the "variants" mentioned above are only variants in the sense of the relationship of their taxonomic features. Animals and plants obviously make up different branches of the overall cladogram of life, the main distinguishing feature being that plants live off sunlight while animals do not. Further subdivisions of both plants and animals would be made on the basis of variations in successively less significant features.
Since features are a product of ancestry, cladograms do strongly follow evolutionary patterns and they would make little sense without assuming common descent, but they are not constructed from evolutionary principles. Hennig's goal was just to reduce the clutter that made taxonomy more difficult, and sometimes led taxonomists to classify organisms on the basis of assumed ancestral relationships that weren't supported by taxonomic features and sometimes didn't exist.
In its early days, cladistics introduced an entirely new level of dispute to the field of taxonomy, though it is generally accepted now. However, these disputes were really not of much interest to outsiders, and taxonomists did not and do not now object to the idea that this enormous array of organisms evolved by natural selection over time, branching out in ever-increasing elaboration from the origins of life billions of years ago.
Some cladistic taxonomists, the "transformed cladists", have dismissed Darwinism as completely irrelevant to their field. Cladistics, in their view, should focus on taxonomic features to the oblivious exclusion of the question of ancestry. Critics of this view reply that it amounts to being overly blinkered and blindered for no particularly constructive reason. In any case, although some taxonomists may seem to say so at times, very few actually see anything wrong with Darwinism itself.
* Pinning down the emergence of the tree of life is not easy. The main evidence is from fossilized organisms dug up from the earth. The first difficulty is that homologies are the only taxonomic tool available for investigation of long-extinct species. Homologies are workable, but they are not in a league with proteins and DNA -- which are, as a rule, only available for species that went extinct recently, and the older the samples, the more difficult they are to examine.
Finding fossils is also troublesome. Fossilization is an unusual circumstance: after most organisms die, they are devoured or decay, and little trace of them is left. Soft-bodied organisms tend to poor candidates for fossils, and so creatures with shells tend to be disproportionately represented in the fossil record. Big creatures tend to be more easily preserved than small ones. Fossilization requires that organisms be neatly buried in sediments, ash, or the like, and left undisturbed while their environment turns into stone. Shallow-water creatures also tend to be disproportionately represented in the fossil record, because the soft bottom sediments of such regions are the most optimum environment for creating fossils.
In addition, it's not likely to find fossils by digging at random; they are generally found in isolated fossil beds. Worse, even stone is impermanent, with geological processes tending to disturb or destroy fossil beds over time, meaning that the older the fossils, the scarcer they tend to be. In fact, it's almost impossible to find undisturbed rocks over about 3.5 billion years old.
Even when fossils are found, they are rarely pristine and detailed, or even complete, some paleontologists describing their most prized fossil finds as "road kills". Still, there have been vast numbers of organisms on this planet, and even if only one in millions survives as a fossil, that still gives plenty of clues. In addition, the fact that geological layers are consecutive, carry signatures in the form of distinctive fossils, and can be dated by radioactive methods allows a chronology to be assigned to these fossil clues. The dating methods allow the relative ages of geologic layers to be pinned down, even when the earth has been flipped over by folding processes, putting the oldest layers on top.
The fossil record, for all its defects, has created a generally consistent vision of just how life has evolved on Earth. Critics make much of the sketchiness and ambiguities of the fossil record, but they are merely attempting to muddy the waters. Although the evidence from archaeological digs is roughly as sketchy and ambiguous, few claim that archaeology is a fraud or compile lists of seeming "anachronisms" -- for example, whiskey bottles buried in ancient Viking settlements -- in archaelogical digs. We have far more hard evidence about, say, the emergence of birds from ground-living reptilian ancestors than we do about the life of Jesus Christ, but only the lunatic fringe claims Jesus Christ was a mythical figure.
Even a sketchy record provides plenty of information. Suppose we take a video, for example an old Charlie Chaplin silent movie, and get a set of consecutively-numbered prints selected at random from about one in every hundred frames -- which is about, on the average, one print per every four seconds of video. That would still be enough to get a general idea of the evolution of the movie's story, though there would be mysteries here and there. Of course, that's assuming that the movie features a coherent, continuously developed narrative. If a movie cut down in this fashion was loaded with flashbacks or completely incoherent, we'd get disjoint images; we'd be hard-pressed to figure out what was going on, and would realize we didn't have a story that made sense.
Similarly, suppose we only know about one in a hundred of the clearly distinct large-scale organisms that have ever existed on the Earth. We still have enough information to get a general idea of the story -- and to see that there is indeed a coherent evolutionary story and not just a set of disjoint images of the past. The fact that there are mysteries here and there does not mean the overall scheme isn't visible. The successive emergence of different types of organisms is very clear, and is not violated.
While critics make much of the sketchiness of the fossil history for particular species, the evolutionary tree becomes increasingly obvious as the taxonomic level rises, and as discussed later there are more than a few specific cases in which the evolutionary evidence at the detail level is actually very impressive. In addition, as new fossils have been discovered, they have generally fleshed out the tree, requiring no more than adjustments in details of the story. Given the current level of activity in fossil-hunting and the availability of good sites, paleontologists believe they are now entering a period where new fossils will be discovered at a rate much greater than in the past -- and would take odds that these new discoveries will also flesh out the story as it is known, and not turn it on its head.
In sum, as far as Darwinism is concerned, the fossil record is not at all a problem, in fact it's all for the good. Nobody who's ever visited even a modest museum of natural history would find its fossil collection a joke; all that has been discovered so far buttresses Darwinism, and the discoveries keep on coming in at an ever-faster rate. The reality is that the fossil record is more generous than we might expect to be, and the only reason the critics are so loud in denying that fact is because it is painfully inconvenient to their agenda.
* It is known from radioactive dating that the Earth is about 4.5 billion years old. The first billion years were unsettled, with a hot, geologically active Earth pounded by impacts of enormous asteroids.
The earliest traces of life are about 3.5 billion years old. Geologists have
long divided the history of the Earth into a set of "eras", which are
subdivided down into "periods" and in some cases "epochs". The different
subdivisions of geological time were originally determined by the fact that
they features distinct sets of fossils. In some cases, the boundaries
between the subdivisions are fuzzy and somewhat arbitrary, but in others the
boundaries are clear-cut, indicating some relatively abrupt change in the
state of the world. The following table gives the subdivisions, with their
beginning dates:
date era period epoch
__________________________________________________________________________
570,000,000 Paleozoic Cambrian
500,000,000 Ordovician
435,000,000 Silurian
410,000,000 Devonian
360,000,000 Carboniferous Mississippian
330,000,000 Pennsylvanian
290,000,000 Permian
__________________________________________________________________________
240,000,000 Mesozoic Triassic
205,000,000 Jurassic
138,000,000 Cretaceous
__________________________________________________________________________
65,000,000 Cenozoic Tertiary Paleocene
54,000,000 Eocene
38,000,000 Oligocene
24,000,000 Miocene
5,000,000 Pliocene
1,500,000 Quaternary Pleistocene
10,000 Holocene
__________________________________________________________________________
The Paleozoic era was preceded by the "Archeozoic" era or "Precambrian"
period, stretching back to the origins of life 3.5 billion years ago, and
beyond through the "Hadean" era when the planet was molten, back to its
creation. Some sources subdivide the Precambrian into multiple periods --
after all, it was much longer than all the later periods put together -- but
for the sake of simplicity, it's given as a single period here.
How life began in the Precambrian remains a mystery, no more than the subject of informed speculations. During the Precambrian, for almost three billion years the Earth was the exclusive property of single-celled organisms. Large multicellular organisms are comparatively a recent invention. However, it should not be thought that nothing much interesting was going on before they made their entrance.
