From Section 3: Informed Organizations

After the eon-spanning excursions of the preceding section, it might be a nice change of pace to return to the beach we were strolling along at the beginning of the chapter. As we resume our aimless wandering we once again notice the rank of palm trees separating the beach from the hardwood forest that clothes the dark flanks of the mountain. Looking out to sea, we can still make out the upper reaches of the coral reef that runs parallel to the shore. And all around us in the vast arena between the reef and the mountains we once again find all manner of creatures occupied with the urgent business of survival. How does what we have learned since our first stroll influence our interpretation of this scene?

Starting from the broad perspective, we now know that all the creatures and communities we recognize around us are linked to their environments, to each other and to countless other creatures and communities by flows of matter and energy that extend throughout the biosphere, and we also know that they all participate in preserving vital aspects of the living Earth, like the oxygen-rich atmosphere. Connectedness remains a prominent theme as we shift our perspective towards the local neighbourhood occupied by communities like the forest and the coral reef - which may meet our standards for recognition as supercommunities - and by more modest collectives like the grasslands fringing the beach and the seaside ponds that teem with life. Within these communities we find a wide variety of interactions involving their constituents and their environments, and once again the bioenergetic facts of life play a prominent role. For example the lichen on the rocks are close associations between fungi that extract nutrients from below and algae that harness energy from the sunlight above, and a similar symbiosis exists between algae and coral polyps.

Not all of the interactions we observe within communities are so intimate or directly connected to bioenergetic exchanges, but many individuals do show a fondness for each other's company, like the monkeys that never go anywhere alone or in silence as they troop through the forest. Other associations appear to owe less to mutual attraction than to shared affinities for the same habitat; for instance during the breeding season many pairs of gulls make nests near each other on patches of seaside grass, where they continually engage in territorial squabbles with their neighbours, whose unguarded chicks they are not above devouring. Even this strained civility is absent among others attracted to the same patch of turf, such the countless seedlings that battle for places within the turf itself, while at the other end of the sociability scale we have the bees, ants and termites that roam far and wide in search of food which they faithfully carry back to their native colonies. Those colonies are highly cohesive, homogeneous and hierarchical, typically consisting of sets of sterile siblings which perform specialized duties - often with bodies shaped specifically to the task - in service of a queen who handles most of the reproductive chores. Social insect colonies also have the unique ability to reproduce themselves, either by propagation - such as when a mated pair of termites founds a new colony - or by division, as when a honeybee colony splits off a swarm consisting of a queen and a retinue of workers who leave to found a new colony.

These tales of birds and bees take us back to our initial discussion of the challenge of sorting out creatures like ourselves, which was largely concerned with criticizing the standard taxonomic approach for its association with an idealistic world view that imposes untenable assumptions upon the living world, such as that species are immutable and eternal. We have since encountered further challenges to the idealistic view of the world, with the most formidable coming in the form of evidence that the living Earth has gone through some profound changes during its lengthy history. Some of those changes have been gradual, like the evolution of the oxygen-rich atmosphere, and some have been relatively sudden, like the great rearrangements when many if not most existing varieties of communities and creatures vanished and then a host of new varieties appeared. These are not the large-scale patterns of change that we would expect to observe in a world governed by ideal unchanging order, and the same applies to the patterns we observe when we shift our attention to more localized aspects of life. For example we have seen that the development of living communities does not conform to the predictions of the superorganism theory, which like the vitalistic theory of embryonic development is based upon the assumption that the patterns we recognize in the living world are shaped, or informed, by forces that originate beyond our earthly plane of reality.

If we accept that creatures like ourselves are not reflections of ideal forms, how do we go about sorting them? Or to put the question in an even less idealistic form: how do they sort themselves? We made a start on answering this question when we compared living communities to their constituents, and noted that there are fundamental differences in their operation, organization and development. Cells come from cells, plants come from plants and animals come from animals, while the patterns we recognize as living communities emerge from interactions among their constituents as they face the ongoing challenge of sustaining viable relationships with each other and their environment. Thus we can think of each community as a unique accumulation of knowledge relating to the survival of a particular set of constituents in a particular environment, or to be less poetic but more thermodynamically correct, we can say that the pattern of each community embodies a unique and dynamic set of information.

We can of course say the same thing about many of the constituents we find within communities; for example we can recognize individual trees because they are unique accumulations of pattern information, as are our own bodies. However, a key difference between communities and their constituents is that in addition to accumulating information, the latter can also preserve it and pass it on in a variety of ways. They can communicate with each other via signals, which can be as simple as alarm calls or as elaborate as the stylized waggle dances honeybees use tell others the location of flowers. Communication can also involve the setting and imitation of examples, as when the mature monkeys in a troop show youngsters what food to eat and where to find it by leading them to the appropriate places at the appropriate times. Such knowledge can be augmented by individual experience, and it can be preserved within cohesive collectives like social groups in the form of cultural information, which has the potential pass down the generations and between groups as they split up, combine, interact or exchange members. Individuals can also preserve and perpetuate information via reproduction; for example when a cell divides, the information content of its physical pattern is portioned among its offspring. Reproduction can also involve the regeneration of complex patterns via epigenesis, where the close resemblance of offspring to their parents indicates that the hereditary information which passes from generation to generation plays an important role in shaping their development.

Lineages

There is certainly no shortage of information in the living world; indeed we could say that information is the stuff of life, because in thermodynamic terms the biomolecules that producers like plants assemble from simpler molecules represent a form of information that is continually being created, passed along, incorporated, altered and destroyed within natural communities. We can use pattern information to recognize individuals ranging from cells to supercommunities and we can use differences in the ability to process biomolecular information as a basis for dividing the constituents of communities into the bioenergetic classes of producers, consumers and recyclers, so it stands to reason that we can recognize further distinctions among living things according to their ability to process, preserve and pass on other kinds of information. For example going back to one of the observations that gave rise to the original biological concept of the species, when horses mate they show us that they share a specific set of hereditary information that is required for the embryonic development of horse embryos, while when donkeys mate they show us that they share a different and equally specific set of information. Thus we can say that horses and donkeys are capable of participating in the perpetuation of distinct and specific sets of hereditary information, or that they belong to different specific lineages.

Thus in place of species our vision of the living world is populated by specific lineages, which requires some minor but important changes to the standard approach to sorting. We can keep the same names - for example the common horse remains Equus domesticus whether the title represents a species or a specific lineage - and we can still rely on many of the standard methods of distinguishing lineages, such as the use of distinctive physical traits (i.e. morphology). However, the crucial difference between sorting species and sorting lineages is that distinctions among the latter are not absolute, and in most cases they are provisional, because making definitive distinctions among lineages involves determining exactly what information they share or do not share. This may seem a subtle point, but if we follow where it leads, some other useful distinctions emerge within the living world.

Suppose, for example, that we are presented with an animal that looks like a mare and another that looks like a stallion; how can we conclusively determine that they are both members of the Equus domesticus lineage? If they are racehorses we can probably trace their pedigrees back through breeding books, and if we turn up one or more common ancestors, that would be sufficient evidence to conclude that they belong to the same extended family, or ancestral lineage, which represents a traceable local branch of the Equus domesticus specific lineage. That would also allow us to describe our horses and their relatives as members of the same ancestral population, which simply means that they are representatives of a common ancestral lineage. For example all thoroughbred racehorses alive today represent an ancestral population derived from three Arabian stallions imported to Britain at the turn of the 18th century, plus a somewhat larger group of English mares.

If we have no information concerning the recent ancestry of our mare and stallion, we could arrange a practical demonstration of their hereditary affiliation by having them mate. If they produce viable offspring that look and behave like them, we can conclude that they share enough horse-specific hereditary information to be interfertile, and if their offspring are also able to reproduce successfully with other horses, then we can conclude that all of the individuals involved in our breeding experiment belong to the horse specific lineage. When we observe similar activities going on in a natural setting, we can say that the individuals involved belong to the same breeding population, which is a group of individuals from the same ancestral and/or specific lineage who engage in practical demonstrations of their hereditary affinities. In principle, it is possible that all of the living representatives of a specific lineage could be members of the same breeding population (assuming that breeding is a part of their normal life cycle), but in the real world it is often the case that local populations are separated from each other by physical barriers, such as mountains, deserts or bodies of water. Populations that are made up of individuals that would be capable of interbreeding but are physically prevented from doing so are referred to as geographic populations.

It is worth noting here that unlike species or specific lineages, we can actually recognize some populations as distinct units within the living world; indeed in many cases they appear to play important roles in the continuation of lineages. For example as was mentioned earlier, orangutans are less sociable than most primates since the long-term bonds they normally form in the wild centre mainly around the lengthy apprenticeship each young ape serves with its mother, and sometimes a sibling or two, before it is ready to move off into its own territory. Yet while most of the orangutans living in a particular tract of rainforest may not spend much time in each other's company they are far from independent, a fact that becomes apparent when local populations become smaller and/or increasingly fragmented, which dramatically increases the probability that they will disappear. Thus when we talk about the long-term survival of orangutans in a given area, we are actually talking about the survival of local populations that must maintain a certain size, density and integrity (i.e. continuity of individual territories) within a supportive environment in order to be sustainable. Any other arrangement of orangutans is not viable outside of a zoo.

If we do not have the time to indulge in breeding experiments with our pedigreeless mare and stallion, nor the opportunity to observe them in a natural setting, the only other way to determine whether they share horse-specific hereditary information is to examine the information itself. We can do this indirectly by looking at the animals, since they represent the physical expression of the hereditary information they possess and perpetuate. Actually, it would be a better idea to first examine a representative sample of horses that we know come from the same specific lineage, in order to see if we can identify one or more physical (i.e. morphological) or behavioural characteristics that are always found in horses, but not in animals from other specific lineages. We can then use these defining traits to identify members of the horse specific lineage, although we may have to live with some uncertainties. For example from my visits to the local zoo I would say that Przhewalski's horse looks more like a donkey or a zebra without stripes than a domestic horse, yet unlike matings with other wild equines, those between domestic and Przhewalski's horses produce fertile offspring.

There are other problems with indirect comparisons of hereditary information, but in this day and age they hardly matter because thanks to modern technology we can now look at some of the actual information that passes from generation to generation. For instance it is a fairly simple matter to distinguish horse cells from donkey cells by looking at them under the microscope, because the nuclei of the former contain 64 of the protein-nucleic acid macromolecular complexes known as chromosomes, while donkey cell nuclei contain 62 chromosomes. In addition to counting them, it is often possible to identify specific chromosomes under the microscope owing to the fact that they have distinctive lengths, shapes and banding patterns when treated with fluorescent stains (the process of counting and sorting chromosomes is known as karyotyping). For example some of the chromosomes in mule cell nuclei (which can vary in number) can be traced back to either their horse or donkey parents.

As anyone who reads the newspaper knows, modern techniques for analyzing hereditary information have gone far beyond karyotyping. Without getting into the details, it is now possible to analyze the macromolecules of living subjects, or those long dead, using tiny samples of blood, bone or tissue, and this information can be used to distinguish lineages, populations, groups, families and even individuals because when it comes to our macromolecules we are all unique. When combined with more traditional approaches the new methods have proven useful in clarifying distinctions among specific lineages and also in determining their affiliations. For example according to protein and DNA analysis the chimpanzee and pygmy chimp lineages can be traced to a common ancestor which they do not share with other ape lineages, hence both varieties of chimps have been assigned to the Pan generic lineage, with chimpanzees being Pan troglodytes and pygmy chimps Pan paniscus.

The tracing of the connections between hereditary lineages is the basis of the systematic classification system, or systematics for short. This system originated at the turn of the 19th century with the great naturalist Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck, who developed a revolutionary vision of the living world based not upon unchanging species but upon lineages that change from generation to generation as adaptations acquired by individuals in the course of their life experience are passed on to their offspring. This theory was not popular among Lamarck's naturalist colleagues, who were mostly of an idealistic bent, and his proposed mechanism of change via the inheritance of acquired characteristics was subsequently challenged by others who were interested in studying change within hereditary lineages. Nevertheless, Lamarck's vision of diverging lineages has played a key role in the development of modern evolutionary thought, and it lies at the heart of the modern systematic classification system, which is based upon the assumption that the more alike the living, dead or fossilized representatives of two distinct lineages are to each other, the more recently those lineages have diverged.

In many cases the distinctions made by systematists are quite similar to those made by classical taxonomists, which is not surprising since the classical system has long recognized that species have obvious affiliations with each other; for example the higher level groupings of species are referred to as tribes, families, and so on. There are, however, some major disagreements between the classification systems, and for that matter among systematists. For instance if we trace the Pan generic lineage back beyond the common ancestor of chimps and pygmy chimps, both major classification schemes agree that it eventually meets up with the Gorilla, Pongo (i.e. orangutan), Hylobates (i.e. gibbons) and Homo (i.e. human) generic lineages, which are all considered to be branches of the familial lineage Hominidae, or apes. The disagreements concern when the particular branches of this family tree separated, and how far apart they have become. In the traditional scheme, which is based largely on morphological and behavioural comparisons, chimps, gorillas and orangutans are grouped in the great ape subfamily (i.e. Pongidae), while humans and their defunct hominid relatives are in another subfamily and the gibbons are off in their own genus. Yet when their affiliations are assessed by biomolecular comparisons, it turns out that the human, chimpanzee and gorilla lineages are more similar to each other than to the orangutans or the gibbons. In fact at a macromolecular level, we are more closely related to chimps and gorillas than the various kinds of gibbons are to each other, so according to some systematists, if gibbons belong to the same generic lineage, then so should Homo gorilla, Homo troglodytes, Homo paniscus and Homo sapiens (relax, it will never happen).

For the record, according to the most complete and current systematic classification I could find, all of the people reading this book belong to the cellular lineage Eukaryota (having large cells with true nuclei and mitochondria), the bioenergetic kingdom lineage Animalia (multicelled, actively mobile biomolecular consumers), phyletic lineage Chordata (animals with backbones or their rudimentary equivalent), subphyletic lineage Vertebrata (chordates with segmented backbones), class lineage Mammalia (vertebrates whose young are suckled), subclass lineage Eutheria (mammals whose fetuses have placentas), order lineage Primates (placental mammals with two mammaries, five digits on each limb, opposable thumbs and collarbones), suborder lineage Anthropoidea (primates with stereo vision and big brains), familial lineage Hominidae (untailed anthropoids with really big brains), subfamilial lineage Homininae (hominids that walk upright), generic lineage Homo (hominines with really, really big brains and small teeth), specific lineage Homo sapiens (the tallest members of Homo with the largest brains) and subspecific lineage Homo sapiens sapiens (Homo sapiens with slender wrists, reduced or absent eye ridges, chins and larynxs suitable for speech).

This classification is essentially a retracing of the evolutionary journey of our lineage from the pre-Palaeozoic era to the point when anthropologically modern humans emerge in the fossil record around a hundred thousand years ago. It has also been possible to trace some of the divergences that have occurred within the human lineage since then; for instance ancestral lineages and populations have been tracked through migrations that have crossed and recrossed the globe. There is a good deal of guesswork involved in this work, as there is in the reconstruction of any historical sequence where each step back introduces new uncertainties, hence it is not surprising that serious differences of opinion have developed concerning what may have happened several generations past, let alone millions of years ago; for example the arguments over how to sort the apes. Nevertheless, the main strength of systematics over the traditional taxonomy is that since its classifications are provisional rather than essential, they can be changed as new evidence becomes available, like biomolecular data or the appearance of previously unknown fossils. For example in the brief time since I first encountered taxonomy in public school there have been two major revisions of the most basic systematic classifications of all, which involve the cellular lineages that gave rise to bacteria (i.e. Eubacteria and Archaebacteria) and eukaryotic cells like ours, and according to today's newspaper yet another realignment is in the works.

One reason there has been so much turmoil in microbiotic taxonomy lately is because recent discoveries have challenged the systematic assumption that long-diverged lineages do not exchange hereditary information. This is probably a reasonable assumption for the most part, but it is not an iron rule. For instance the founder of the bread wheat lineage (Triticum aestivum) appears to have been a viable hybrid prodded by the fortuitous combination of gametes from two different types of grasses, and there is ample molecular evidence of parcels of hereditary information being be exchanged between specific lineages of bacteria and even between phyletic lineages, such as bacteria and fungi. It has been proposed that in the distant past it was easier for long-separated cellular lineages to exchange hereditary information, and in some cases they may have physically combined to produce chimeric lineages. Indeed according the endosymbiont hypothesis, eukaryotic cells emerged from a series of combinations and exchanges among several lineages of ancient cells, with the partners taking on specialized duties as they lost their independence; for example photosynthetic bacteria may have become the chloroplasts of eukaryotic algae.....