The geological theory of the evolution of the material environment and the biological theory of the evolution of organisms by natural selection are usually treated separately. This paper presents a new evolutionary theory, in which the evolution of the organisms, and the evolution of their material environment, are seen to be so closely coupled as to form a single, indivisible, process. This combined evolutionary system can be taken to be a domain with emergent properties unexpected from a simple addition of its component parts, rather like the eighteenth-century scientific view of the Earth as a super-organism. In homage to James Hutton, who lectured before the Royal Society of Edinburgh about the Earth as a super-organism and on the physiology of the Earth, the new topic is called geophysiology.

The difference between the geophysiological view of the Earth, where the environment and the organisms are tightly coupled, and the co-evolutionary, or biogeochemical view, where the coupling is loose leaving organisms and their environment to evolve more or less separately, is discussed. The paper includes numerical models to illustrate how a close-coupled evolutionary system could have self regulation, homeostasis, as an automatic and emergent property. The models will be compared with the real world past and present and their predictions examined.

There is a general consensus that the global chemistry of ocean water has not changed markedly during the Phanerozoic. Nevertheless, significant changes have occurred in the geochemical cycles of some elements and patterns of change have been reconstructed, in various forms, through consideration of the isotope ratios 13C/12C, 34S/32S, 87Sr/86Sr and 143Nd/144Nd. There have also been attempts to constrain variations in the isotopic composition of sea water itself through measurements of D/H and 18O/16O, the latter both directly and indirectly. Dissolved constituents in seawater display secular changes in isotopic composition as a consequence of quite different driving mechanisms. δ13C and δ34S variations are broadly correlated and linked by carbon and sulphur exogenic cycle interaction through redox reactions (the “free oxygen cycle”). The 87Sr/86Sr trend is determined by the balance among different Sr inputs to the oceanic pool, which vary in their isotopic composition (limestones, old granitic material and young basaltic material). Neodymium isotope variations are not globally synchronous. Changes in 143Nd/144Nd are influenced by local erosion products from continental landmasses and can therefore be different for coexisting palaeocean basins.

Fossil assemblages can give quantitative estimates of palaeotemperatures, by comparison with modern biota, only in the recent geological past. Oxygen isotopic palaeotemperatures on calcareous or phosphatic fossils are potentially available for the whole Phanerozoic. Their reliability is limited by physiological effects (generally believed minor), preservation (for which criteria are available), and by uncertainty in the isotopic composition of ancient seawater. The latter is greatly affected by glaciation. In the Cenozoic, the relative contribution of ice-volume change and temperature change in producing isotopic variations can largely be resolved by analysing planktonic and benthic foraminifera in deep-sea cores. For earlier times only continental shelf deposits are available. In the Mesozoic, reasonable assumptions about ocean isotopic composition lead to palaeotemperature estimates that suggest generally higher temperatures than at present, particularly for mid- to high latitudes. This agrees with estimates based on biotic distributions. Late Palaeozoic glaciation is reflected in variable isotopic compositions in high palaeolatitude areas. In the earlier Palaeozoic, well-preserved fossils indicate either oceans enriched in 16O compared to today's or generally higher temperatures; controversy continues about the relative importance of the two effects.

The basic properties of living systems are remarkably consistent and involve energy interactions between intracellular and extracellular environments. These interactions predispose living systems to deposit minerals from many solutions. The evolution of biomineralisation was not a single cellular invention but rather the association and perfection of a few of these fundamental properties of cell biology. The components of biomineralisation systems involve some mechanism for modifying the activity of at least one ion, an interface for initiating and possibly controlling crystal growth, a diffusion limited size and a mechanism for manipulating the growth of the crystal lattice. The evolution of these components of biomineralisation in the context of geological time inevitably concentrates on the Precambrian–Cambrian boundary. Over a time scale of less than 50 × 106 years there was a proliferation of metazoan phyla, the mineralisation in a large number of taxa and the exploitation of a diverse set of processes involving agglutinated sediments, silica, phosphates and carbonates. A large number of theories have been proposed to explain why biomineralisation occurred at this particular time. Such theories should recognise the importance of the incorporation of the citric acid cycle into the cellular metabolism of many organisms and its exploitation in an aerobic environment, the development of multicellularity which enormously increased the opportunities for modifying ion activities in diffusion-limited sites, and the exploitation of browsing and carnivorous feeding habits. These influences had major effects on ecosystems and population structures and put considerable selective pressure on the advantages that could be gained from a skeleton.

Although many physiological characteristics are very labile, it is proposed that some are stable enough to provide evidence concerning the routes by which terrestrial animals moved on to land. Osmotic tolerance and osmoregulatory ability are investigated first. Marine littoral invertebrates tolerate wide osmotic changes but osmoregulate little. Freshwater invertebrates osmoregulate well, but over a narrow range. Terrestrial prosobranchs of the family Pomatiasidae, which have wide tolerance, may have originated directly from the sea. The Cyclophoridae, which are intolerant, may have moved to land from fresh water. Isopods and talitrid amphipods may all have had direct marine origins with no freshwater phase. Secondly, terrestrial animals of marine origin may have blood with higher osmotic pressures than those passing through fresh water. In prosobranchs, isopods and amphipods, the evidence agrees with the conclusions suggested from character one. Thirdly, the production of hypo-osmotic urine in terrestrial animals may be evidence of freshwater origin. The evidence again supports the initial suggestions about prosobranchs and amphipods. It is concluded that because there is little selection pressure acting on these characters on land, they can be used as evidence of ancestry. Possible use of further characters is discussed.

The ecological ranges of Archaeobacteria and Eubacteria are constrained by a requirement for liquid water and the physico-chemical stability limits of biomolecules, but within this broad envelope, prokaryotes have evolved adaptations that permit them to tolerate a remarkable spectrum of habitats. Laboratory experiments indicate that prokaryotes can adapt rapidly to novel environmental conditions, yet geological studies suggest early diversification and long-term stasis within the prokaryotic kingdoms. These apparently contradictory perspectives can be reconciled by understanding that, in general, rates and patterns of prokaryotic evolution reflect the developmental history of the Earth's surface environments. Our understanding of modern microbial ecology provides a lens through which our accumulating knowledge of physiology, molecular phylogeny and the Earth's history can be integrated and focussed on the phenomenon of prokaryotic evolution.

When compared with sea water, most marine invertebrates are isosmotic but show varying degrees of ionic regulation, from accumulation of potassium and calcium to reductions of magnesium and sulphate. A reduction of sulphate in pelagic animals such as jellyfish and salps, and an accumulation of ammonium ions in arrow-worms (Sagitta) contribute to their near-neutral buoyancy. Marked reductions in salinity exclude mahy marine invertebrates. In the Baltic, polychaetes, bivalve molluscs and decapod crustaceans are reduced from 193, ninety-two and sixty-four species in the Belt Sea (salinity S 10-30‰) to three, four and two in the Gulf of Finland (salinity S 5-9‰). The chelicerate Limulus can stand a wide range in salinity, a few insect larvae can tolerate concentrations of 200% sea water, while the branchiopod shrimp Artemia can stand crystallising brine (36-37% NaCl). Very few species can tolerate temperatures of 40°C. One such species is the polychaete Alvinella pompejana, a hydrothermal vent animal at East Pacific Ridge (to the W of S America). The harpacticid copepod Tigriopus living in evaporating rockpools has a lethal temperature of 42°C at a salinity of S 90‰, but at S 8‰ that temperature is 34°C. Lack of oxygen and presence of hydrogen sulphide limit the distribution of animals in certain areas. Most active animals have respiratory pigments in their principal body fluid. Burrowing invertebrates such as Arenicola and Lingula have respectively haemoglobin in the blood and haemerythrin in the coelomic fluid, with mean oxygen capacities of 6 ml O2 per 100 ml in each case, compared to 0·6 and 0·5 ml in sea water at 10° and 20°C.

The nature of the fauna of brackish-water environments is reviewed. It is concluded that: (a) a specific brackish-water macrofauna does not exist; (b) in salinities of >c. 5-8‰ the fauna is one that also occurs in soft sediments under fully marine conditions when circumstances (possibly the absence of competing species) permit; (c) in salinities of <c. 5‰ the fauna is essentially a freshwater one; and (d) inability to cope physiologically with brackish water is not a factor of major importance in limiting species diversity in these habitats, except in the vicinity of 5‰ salinity. Caution is therefore advised in assigning brackish status to past environments on the basis of their preserved fauna.

The modes of life and environments of the extant agnathans (cyclostomes) are discussed in relation to their adaptations to temperature, light, oxygen and salinity. As their antitropical distribution indicates, both hagfishes and lampreys are cold water groups. Since hagfishes live in deeper waters than lampreys, they are not exposed to the marked seasonal changes in temperature and light which influence major events in the lamprey life cycle. Both groups tend to be nocturnally active, either burrowing during daylight as in the case of larval lampreys (ammocoetes) and most hagfishes, or showing cryptic behaviour as in the case of adult lampreys. Olfaction plays a major part in the location of prey, presumably aided in adult lampreys by their eyes and sensitive electrosensory system. Rates of standard oxygen consumption, ventilatory frequency and heart rate of adult lampreys increase at night. Standard oxygen consumption is relatively low in ammocoetes (as it also is in hagfishes) but increases markedly during metamorphosis into the adult lamprey. Ammocoetes and hagfishes, and to a lesser extent adult lampreys, are resistant to reduced environmental oxygen tensions. Differences in the oxygen dissociation curves of ammocoetes, adult lampreys and hagfishes can be related to differences in the characteristics of their monomeric haemoglobins and their environments and modes of life. The extraordinary tolerance of the hagfish heart to hypoxia is a reflection of a robust capacity for glycolysis, an LDH isozyme geared towards anaerobic functioning and a low work output. The hagfishes, which are restricted to marine waters, are osmoconformers. The osmolality of their blood, which is almost wholly attributable to inorganic ions, is virtually identical to that of full strength sea water (c. 1000 mOsmkg−1). By contrast, the osmolality of the blood of larval and adult lampreys when in fresh water is only 205-260 mOsm kg−1, i.e. about one quarter to one fifth of those of hagfish, and these rise only to 240-270 mOsm kg−1 in the adults of anadromous lampreys in sea water. The regulation of ions by adult lampreys is achieved by mechanisms similar to those adopted by teleosts. The implications of the contrasting ionic and osmotic physiology of the two living groups of agnathans are discussed in relation to their possible environmental history and against the background of their Carboniferous fossil representatives.

Ash-free-dry-weight determinations for a representative range of living brachiopod genera have revealed that a consistently high proportion of total organic mass is contained within the shell, partly as the organic matrix for biomineralisation and partly as minute extensions of the mantle tissues (caeca) housed within hollow endopunctae permeating the shell. On average 40% to 50% of the total organic mass of both articulate and inarticulate brachiopods is situated within the shell. This is true even for a rhynchonellid brachiopod which does not possess endopunctae, but which has a more dense protein matrix in its shell. The effectively hidden constituent of brachiopod tissue mass which is included in this component has often been overlooked, and as a result total metabolic tissue mass has been underestimated. This throws into question some previous interpretations of brachiopod respiratory and metabolic data.

The oxygen consumption rates of several living brachiopods have been measured, and when respiring tissue in caeca in the shell is taken into consideration, it is clear that brachiopod metabolic rates are low when compared with other marine invertebrates (e.g. between 10% and 50% of the oxygen uptake of comparable gastropods and bivalve molluscs held in similar conditions). This low rate cannot be attributed to a slower pumping rate by the brachiopod lophophore, as has been suggested, because the rate of water movement is comparable to that across the bivalve gill.

Nitrogen excretion rates have also been measured for a few living brachiopods, allowing a comparison with rates of oxygen consumption and providing an indication of the metabolic substrates used. These data on oxygen: nitrogen ratios suggest that one Antarctic brachiopod utilises exclusively protein as a metabolic substrate, while a temperate latitude species uses mainly protein during winter but lipids and carbohydrates during summer months. Histological observations, particularly of Terebratulina retusa from temperate waters, show that a specialised tissue layer in the brachiopod outer mantle epithelium proximal to the shell may be the site of storage of the protein that is metabolised during winter, and of carbohydrate mobilised during gonadal development in summer. The caeca have also been suggested as sites of storage of metabolites, and the possible relationships between these areas of mantle are discussed. It seems that the ability to store nutrients in the mantle, combined with flexibility of substrate utilisation and an inherently low metabolic rate, have been important factors in brachiopod evolution.

Present-day organisms have colonised two distinct high pressure environments: the deep sea and oil well and other crustal fluids. In the former, pressures attain 100 MPa and temperatures are generally less than 4°C. In the latter, the temperatures are high, up to 150°C, and occur in combination with pressures of up to 50 MPa. The high temperature is close to the limit of thermal stability of the macromolecules essential for life. The adaptation of present-day marine organisms to high pressure is known to involve modifications to their cell membrane lipids and subtle changes in both structural proteins and enzymes. There is no reason to suppose that they are close to the maximum pressure to which they could adapt and higher pressures could have been colonised in the geological past. The existence of “marker” compounds, characteristic of high pressure organisms, is discussed, and the possibility that isotope ratios are distorted by metabolic processes at high pressure is raised.

Discoveries, most of them recently, in more than thirty Lower and Middle Cambrian horizons with soft-bodied fossils have shown that forty-one of the genera occur also in the celebrated Burgess Shale (Middle Cambrian). Significantly, they tend to have lengthy stratigraphic durations which together encompass an interval from the early Lower Cambrian (Tommotian) to near the end of the Middle Cambrian. At least some genera have also wide geographical ranges, with occurrences around much of the Laurentian (N America) craton, and also in N and S China, Australia, Siberia, Spain and Poland. Although a few genera, e.g. Isoxys, may have been pelagic, for the most part these distributions are explained in terms of a deeper-water biota with an evolutionarily conservative aspect. Both the origins and further recruitment to this biota may have been from shallower water, with more limited in situ diversification. It is speculated that this distinctive Cambrian biota was gradually driven to extinction with the arrival of Ordovician competitors, although some relics may have survived until at least the Devonian. This history has implications for our understanding of deeper-water faunas throughout the Phanerozoic, and supports the notion that archaic forms may take refuge in this environment.

Examples of the mechanisms involved in body fluid regulation by present-day crustaceans inhabiting variable salinity habitats are described using amphipod gammarids and the isopod Mesidotea (Saduria) entomon as models. Appropriately the species inhabiting the most demanding habitats have the greatest range and most sophisticated regulatory responses. Behaviour, micromorphology and physiology are all involved to a variable degree and, in the examples discussed, responses to salinity change seem finely tuned to countering the problems generated by particular environments. This applies both in the rapid responses to sudden alteration in salinity and to the longer term changes associated with acclimation to a new steady state condition. The isolation of populations and features of derived freshwater races are considered and the implications for the presumed physiological mechanisms of fossil forms discussed.

Shrimp-like malacostracan crustaceans first appeared in the late Devonian and underwent a substantial adaptive radiation in the Carboniferous. They are rarely found in rocks of fully marine origin but are well represented in sediments laid down in brackish water and marginal marine conditions; such transitional environments provide the exceptional circumstances required for the preservation of unmineralised shrimps. The best examples are in the Dinantian of Scotland, the Namurian of Montana, and the Westphalian of Illinois. It is probable that shrimps were widespread in contemporaneous marine environments, but are not preserved.

Any approach to understanding the physiology of fossil organisms is necessarily indirect. The diversity of crustacean communities, and the nature of associated taxa and trace fossils, are the most useful biotic factors for interpreting the habitat and tolerance of fossil examples.

All known Carboniferous crustacean communities lived in brackish conditions; none is fully marine. Malacostracan assemblages in the Dinantian of Britain show a general trend of increasing diversity with salinity, from a single taxon at Gullane (stratified freshwater lake or brackish lagoon) to ten at Glencartholm (approaching normal marine). Tealliocaris is associated with low salinities. Crangopsis socialis is confined to the brackish water interdistributary bay environment, but Bairdops and Belotelson display a broader environmental tolerance. Crangopsis eskdalensis, Sairocaris, and Perimecturus occur only at Glencartholm, indicating a requirement for a strong marine influence. Those taxa confined to a limited environmental range all occur where a marine influence is pronounced; none occurs solely in areas of lower salinity. While salinity was apparently the dominant influence on distribution, a complex of independently varying environmental factors was involved. The range of habitats colonised early in the Carboniferous indicates that the preserved taxa had already developed advanced osmoregulatory mechanisms.

The wide range of organs of respiration (book-gills, book-lungs, sieve- and tube-tracheae), reproduction, sensory perception, etc., among the chelicerates indicates that the major groups made the transition to land life independently. The fossil record is patchy for most chelicerate groups, certain intervals (e.g. Westphalian) being particularly rich in chelicerate bearing Lagerstatten while in others (e.g. Mesozoic) they are sparse. Due, apparently, to their unusual hyaline exocuticle, scorpions are better preserved than other arthropods, and show a fairly continuous record from fully aquatic forms in the Silurian, to both aquatic and terrestrial faunas in the Carboniferous. In particular, new and well-preserved material of the earliest demonstrably terrestrial scorpions from the Lower Carboniferous of East Kirkton, West Lothian, suggests that book-lungs, at least in the scorpions, developed directly from book-gills by suturing of the covering plate (Blattfuss of the related eurypterids) to leave stigmata for diffusion of air. This evidence supports the ideas of early authors that the scorpion mesosomal ‘sternites’ are fused plates, contra Kjellesvig-Waering (1986) who envisaged the plates being lost to reveal true sternites beneath. The fossil evidence also indicates that by the Triassic at least two scorpion lineages had evolved intra-‘sternite’ stigmata.

Flight—defined as the ability to produce useful aerodynamic forces by flapping wings—is one of the most demanding adaptations in vertebrates. The mechanical problems of flight ensure considerable external morphological homogeneity and behavioural similarity in extant fliers. Observations of the vortex wakes and wingbeat geometry of modern birds and bats confirm that the two groups are mechanically very similar, despite differences in phylogeny, anatomy and physiology. With this background it is possible to attack two problems: the evolution of flight in vertebrates, and the flight performance of extinct animals such as pterosaurs and Archaeopteryx.

The origin of flight has been surrounded by considerable controversy, due in part to terminological inconsistencies, in part to phylogenetic uncertainty over the relationships of birds, bats and pterosaurs, in part to disagreement over the interpretation of the available fossil evidence, and in part to argument over the relative importance of morphological, mechanical and ecological specialisations. The mechanical changes needed in the course of the evolution of flight favour a gliding origin of tetrapod flight, and on mechanical and ecological grounds the alternative cursorial hypothesis may be discounted. This argument is particularly strong in bats, but has been thought to be weaker in birds owing to apparent inconsistencies with the fossil evidence. However, fossils of the Jurassic theropod dinosaur Archaeopteryx also support a gliding origin for flight, and suggest that this animal was adapted for flapping flight at moderately high speeds associated with gliding; it could fly less well at the slow speeds which would have been required for incipient flight in a running cursor, and at which the wingbeat is aerodynamically and kinematically considerably more complex. Slow flight in birds and bats is the more derived condition, and vertebrate flapping flight apparently evolved through a gliding stage.

The pterosaurs have become the subject of much controversy over the nature of their stance, the wing surface, and the degree of involvement of the leg in the wing membrane. Reconstruction of their wings indicates proficient flying animals, and comparison with birds suggests that most pterosaurs probably occupied marine or coastal/estuarine habitat.

The spatially fixed sporophyte body of vascular land plants has to be adapted to both atmospheric and substrate environments. Potentially almost all stages in the life cycle of a land plant are fossilisable and the physiological adaptations to these environments are reflected in the morphology, anatomy, and chemistry of the plant. Although solutions to the plant's physiological problems have been refined through evolution, the basic responses to fundamental environmental parameters such as temperature, water availability, nutrient supply, gas exchange and light, evolved early in land plant history. These taxon-independent solutions can be used qualitatively, and sometimes quantitatively, to track changes in atmospheric and edaphic conditions throughout much of the Phanerozoic. Increase in body size and height in Middle and Late Devonian times was coupled with intense demand for light, nutrients and water supply and with elaborations of vascular systems, photosynthetic surfaces, organ abscission and ‘root’ organisation. During the Carboniferous extreme adaptations to substrate waterlogging evolved. Mycorrhizal associations and “phi” layers in Triassic roots represent early aspects of modern root physiology. From the mid-Cretaceous, angiosperms exhibit leaf architectural characteristics which in modern plants relate qualitatively to moisture and light, and quantitatively to temperature, while vessel size and distribution in trunk wood is related to water stress and susceptibility to freezing. The relative proportion of plants utilising C3, CAM, and C4 photosynthetic pathways varies with environment. Isotopic analysis of plant fossils may demonstrate changing relative frequencies of photosynthetic pathways through time in relation to atmospheric composition and temperature.