On Earth (and presumably elsewhere in the universe), groups of organisms show different levels of relatedness: different species of maple trees are all more closely related to each other than any are to the oaks, but oaks and maples are more closely related to each other than they are to pines, spruces or firs, which are in turn closely related to each other. Oaks and maples share a common ancestry because they are flowering plants. Pines, spruces and firs share a close common ancestry as conifers. The two groups of trees also share a common, but more distant ancestry as seed plants. They share an even older relationship with a larger group of plants, the vascular plants, those that possess xylem and phloem, tissues specialized to transport water and nutrients within the plant. Given evidence in the form of the characteristics of oaks, maples, pines, spruces and firs, a “family tree” illustrating relationships among these plants can be generated.

On a larger scale, all of the green plants share common characteristics, such as their chlorophylls and cell walls of cellulose, which they do not share with animals or fungi. All of the complex, multicellular (and many single-celled) organisms on our planet are called eukaryotes (or eucaryotes) because their cells have membrane-bound nuclei within them where much of their genetic material is housed. It doesn’t matter if they are plants or animals; eukaryotic creatures all share this feature of keeping their chromosomes tucked within a nucleus surrounded with a membrane. Excluding some phloem cells, some red blood cells or others where the nucleus becomes degraded or disappears as the cell matures, there are no exceptions, no evidence to falsify this feature of nucleated cells as capable of grouping an otherwise diverse array of organisms. The possession of nucleated cells by such a vast and varied collection of creatures suggests an ancient relationship that branched after the point of evolution of eukaryotes, generating through irreversible change, increasing complexity and divergence through time, all sorts of creatures. The fossil record and related geological evidence offer additional, powerful corroboration, that evolution has been going on for a few billion years. Many of the species that once inhabited the Earth no longer exist, but they once evolved and then persisted for a time. Present-day species are related to some of the extinct ones, and this can be demonstrated through various sources of evidence, comparative biology, including DNA (when available).

Some characteristics, such as eukaryotic cells, the ubiquitous proteins that serve as enzymes, and informational molecules such as DNA or RNA are shared among great numbers of organisms. Unless we have evidence to suggest otherwise, we assume these shared characters are truly shared, that they are homologous, that they came into existence only once and have been carried along with the diverging lineages that trace evolutionary time. Sometimes, given relevant evidence, similar features can be shown to be mere analogs that may share a function, but not an evolutionary origin. The forelimbs of horses, cats, humans and birds are homologs, but the wings of birds and insects are analogs – they both function in flight, but appeared independently. This is convergent evolution – two structures that share the same function, but have different origins. Homologous features such as nucleated cells provide evidence that life forms as different as mushrooms, mosses, oak trees, earthworms and humans all share a very old common ancestry. However, there is also evidence suggesting that early life on Earth arose more than once. Jack Maze adds, “The origin of life is a very contentious issue in biology and the argument for a single origin of life is being questioned. Data gathered by some microbiologists, those who study the smallest living creatures, indicate that life arose more than once, resulting in a ‘pool’ of simple organisms from which diverse lineages arose. The idea that life has arisen several times is appealing since it implies that life is the result of the action of natural laws. Also, the argument that life arose only once gives that event the property of a miracle, a completely unique event that is not repeated. Miracles are the result of divine intervention, something to be rejected in offering an account of the natural world.”

Systematists, as they seek to understand evolutionary relationships among species and higher groups, generate branched diagrams that look something like family trees. Historically, different methodologies have been used to clarify relationships among species, or at least to group them in some sort of natural manner. As the scientists and naturalists of the 18th century began to collect and catalog organisms, they noticed the fossils they were finding represented ancient life forms that were both like and unlike the living organisms around them. Life forms were somehow connected, they realized. Elucidating the “great chain of being” was at first an attempt to understand, and so better appreciate, God’s creation. The early systematists grouped organisms based on the characters they possessed (or sometimes didn’t possess), but this was (and continues to be) difficult. Linnaeus, who developed the binomial system of nomenclature we continue to use, where every species has both a genus name and a species name, tried to discover the natural affinities of plants. He grouped them based on such characters as the number of stamens on a flower, but he wasn’t satisfied with the result and realized that some of his groups were artificial, that they didn’t fully reflect actual patterns of nature.

A century or so later, once Darwin’s theory caught on and biologists began to understand something of genetics; systematics was done within an evolutionary context. This approach was known as evolutionary systematics, and it tried to tie the adaptation and natural selection assumptions of neo-Darwinian theory to hypothetical relationships among species, with variable results. One of the problems was that this method relied too much on the expertise and opinion of the biologist – it was perfectly acceptable to declare that species X was most closely related to species Y because you, the expert, said so, even when the evidence was weak. (Like the famous line from the movie, "Ghostbusters" – “Back off, man! I’m a scientist!”) Sometimes characteristics were assumed to have evolved more recently if they appeared to be “adaptive” from an engineering standpoint, or just seemed clever. A problem here is when a theory is used to test data rather than the other way around. Actually, many of these biologists, the evolutionary systematists, had such a thorough knowledge of their groups of organisms that their assertions were later corroborated. Even so, it’s always better to have some evidence to back up even the most educated intuition.

With the rise of computers in the 1970s, a new approach to systematics quickly gained popularity. This approach was called numerical taxonomy or phenetics and it relied on a computer to generate a tree showing hypothetical relationships. On the one hand, the numerical taxonomists had a good point: “Show me the data.” But on the other hand the method was weakened by the underlying assumption that all data, all characters were equally relevant and relationships among species could be based on their overall similarities. Many present day systematists who rely on molecular data take a phenetic approach in looking for overall similarities.

In the 1950s a German biologist, Willi Hennig, developed a third approach to systematics, called phylogenetic systematics or cladistics (Phylogenetic Systematics…need rest of ref). This method, which didn’t begin to reach a larger audience until the 1970s, relies on relevant evidence, or at least it tries to. Cladistics limits the assumptions that can be made about the characteristics of an organism; it tries to exclude conjectures about the relative importance of perceived “adaptations.” The existence of homologous features is assumed to be real – that the wings of birds evolved only once from earlier forelimbs, and that all birds share this unique feature of bird wings, whether the wings function or not. Cladistics also assumes that evolution – speciation or lineage splitting or phylogenesis – happens, but cladistics is more concerned with the resulting pattern of relationships and less with the how or why. Using this method, trees (called cladograms – a clade is a collection of related species or groups that share a common ancestry) are produced that illustrate evolutionary relationships. Classical cladistics is quite rigorous and requires that the characters used to unite two or more species or larger groups be shown on the tree. It is also expected that any characters that provide falsifying evidence for the cladogram should likewise be displayed.

Although they can be annoying, cladistics uses a set of terms that are used to classify and clarify the characters used to group organisms together. An autapomorphy is a characteristic shared by all of the individuals in a single species. An autapomorphy can be physical or behavioral and it helps to define the species, but doesn’t clarify the relationships of one species to other species. A synapomorphy is a character that is uniquely shared by a group of species and defines that group, or at least gives it empirical support. When we look at all of the animals, only mammals have hair. Hair is a synapomorphy for mammals and helps to define the group. A plesiomorphy is also a shared characteristic, but is too broad – it is shared by too many species to help define relationships within the smaller group being studied. Mammals have backbones, but so do other animals that are not mammals, so the presence of a backbone doesn’t help us to sort out the relationships among mammals. If we expand the view to a more inclusive scale and look at all of the animals in the world, including insects, sponges and worms, then the possession of a backbone becomes a defining synapomorphy for one subgroup of animals, the vertebrates. But if we are interested only in mammals, the presence of a backbone is a plesiomorphy because it gives no new information, and no information at all about the relationships among mammals, unless the particular details of backbones are more closely examined. We already know that all mammals are vertebrates. Whether a character is considered a synapomorphy or a plesiomorphy depends on the scale of the systematic study.

When properly done, cladistics demands even more. How do you know that what you have is really a synapomorphy, that it identifies a unique group? Only by comparing the group you are studying (the ingroup) with more distantly related groups (called outgroups) can synapomorphies be legitimately identified. Outgroup comparison allows systematists to discover which characters or character states of the ingroup species are most ancient or more recent. These comparisons also help systematists identify variables that are irrelevant because they are too inclusive (plesiomorphies) or too exclusive (autapomorphies). The clearest characters are those that obviously define a group because they don’t exist elsewhere in living things – no outgroup has that character or character state. Animals with backbones are a pretty well defined group, as are the mammals and the flowering plants. Defined by clear and unique features, each of these groups gives us good reason to assume they are real. John Lynch coined the term “universal synapomorphy” to describe these clearly delimited features. Unfortunately, the tidy evidence we would love to have is often all too rare, especially in such wildly variable creatures as plants. Molecular data can be similarly unclear. DNA evidence is often more useful in identifying the unique characteristics of individuals, families or populations than the relationships among species, partly because we don't understand how much of the information in DNA is housed or expressed.

This way of looking at relationships among species, where evidence of membership in a group consists of characters, synapomorphies, shared only by the members of the group, is the basis and the strength of phylogenetic systematics or cladistics. The goal is to construct a tree or cladogram where the branches of the tree are species (or genera, etc.) and the branching pattern is defined by nested sets of uniquely shared characteristics that describe each subgroup. The idea is similar to set theory in algebra – instead of a tree, the same information can be depicted as nested sets within brackets. The set of primates can be defined by their own unique characteristics. Primates can be nested within the larger group that includes all mammals, and the mammals can be nested within the larger set of all vertebrates. At each level there are criteria, specific characteristics, synapomorphies that define membership in each group.

Cladistics properly done doesn’t automatically label as “advanced” what might look to us like clever “adaptations” because this invites unnecessary subjectivity. The evidence gained from comparative studies, especially from outgroup comparison, is what matters. As cladistics became popular in the 1970s and ‘80s some cladists, though they generally did not offer any alternatives to neo-Darwinian theory, were highly critical of the use of “adaptations” when deciding on which traits were most ancient or more recent (this is known as character polarity). The cladists preferred that character states for the group of organisms being studied, the ingroup, be assessed by comparison with the more distantly related outgroups without judging any apparent cleverness of character states. Deciding that a particular character was “advanced” before looking at the entire dataset, the ingroup of interest plus the outgroup(s), could lead to biased conclusions, they argued, and this constituted poor scientific methodology. One example (from Nelson & Platnick? – find ref) had to do with phylogenetic relationships among spiders. To us humans, the webs of the orb-weaving spiders seem like such nice pieces of engineering (and so photogenic when covered with dew or frost) that they must be advanced when compared with the messier webs of the cob-weavers. However, when all of the relevant evidence is considered, and no character is given extra weight because of its good looks, the orb-weavers are identified as the more ancient group, while the messy cob-spinners appear to be more recently evolved. In reality, either style of web is capable of capturing insects, but the theory-laden views of some of the evolutionary systematists compelled them to consider an orb type web as better adapted, better looking, and therefore more “advanced.”

Some cladists asserted that they needed no theories of evolution in order to accurately describe relationships among species and higher groups – all they needed were good datasets. In fact, to approach any study of relationships by looking for assumed adaptations, they argued, was so theory-laden that it would lead to biased studies that were unnecessarily difficult to test, improve or falsify. Many evolutionary biologists and theoretical ecologists were horrified – if these cladists weren’t believers in neo-Darwinian theory, then they must be creationists! The atheoretical cladists weren’t creationists at all, but they weren’t too fond of neo-Darwinian theory either. Some were very uncomfortable with the idea that you should interpret your biological data in such a way that they agree with a particular theory. This is backward, they insisted – you must first gather and analyze the data and construct a phylogeny, a hypothetical tree depicting the relationships among species. After that, it is legitimate to use the cladogram to test assumptions about evolution. You can judge a theory based on evidence, but you can’t judge evidence, data or facts based on a theory. To ignore relevant data, especially when it could blow up a hypothesis or theory, might be tempting, but it’s not very principled.

For too long, it’s been neo-Darwinians versus creationists with no other options. In creating this false dichotomy, perhaps the neo-Darwinians were acting to “protect their turf” of evolutionary biology. But this reaction only serves to close off the search for alternatives, for possible causes of evolution beyond natural selection and adaptation. It’s just damn bad science. Jack says: “And it’s interesting that some of the modern critics of evolution, those of the Intelligent Design movement, rely on natural selection being of relevance in evolutionary theory, and so base much of their attack on the inadequacies of natural selection. Were an alternate theory available, the IDers would be dead in the water.”