The discovery of the ATGC+U coding in DNA and RNA opened up ways of assessing the relatedness of organisms without relying on their outward appearance. The more closely related two organisms are the more similar are their base sequences, and vice versa. Because a significant part of the base sequence or genome of all modern life forms that have been analysed is the same, all are related. The differences all materialised through genetic mutation at some time in the past. The greater the differences between the genomes of any two organisms, i.e. the larger the number of mutations accumulated since their lines of descent split, the further back in time they shared a common ancestor. Their sequences survive because those mutations and others in the same sequence either conferred fitness, or had no consequence as regards survival and reproduction.
If two groups diverge from a common ancestor they start out genetically very similar, but collect mutations independently and at random. The passage of time ensures that their genetic material becomes increasingly different. This is based on two simple assumptions. First, that genes ceased to pass between the two populations – a widely used basis for defining separate species. Second, as the range of options for mutations is large, the same set of mutations are vanishingly unlikely to form more than once. The second premise is impregnable, but there is a problem with the first in some types of organism. For the moment we shall stick with the assumptions. Accumulation of differences with time suggests that there may be a way of going beyond the degree of relatedness to establish a molecular clock that shows when divergences began. Simply count the number of differences in some genetic material, assume a constant rate of mutation, calibrate that somehow and you have a timing device.
Such a seemingly obvious evolutionary stopwatch must have a snag, and it does. The problem is natural selection itself. Although mutations occur randomly – that is, new ones are likely to appear at equally spaced intervals – those which survive have passed a selection process, which is non-random. A threatening or disadvantageous mutation soon disappears, whereas one that increases fitness or has no effect either way lives on. It can spread through populations quickly and so speed up the rate at which groups diverge genetically. Advantageous genes appear and spread at variable rates, and that is the last thing needed in any kind of clock. Several factors get around this obstacle.
Mutations have no built-in reason for being influenced by natural selection; they are just changes. So some are neutral. Changes in the amino acid sequence in one or other protein can leave its function unchanged. Other neutral mutations merely alter the amounts of the chemical products of transcription, having no effect on their structure. Above all, much DNA is not even transcribed in the first place, and these ‘mute’ sections are transmitted down the chain of generations and accumulate mutations at random. Since they have no function they neither cause problems nor produce opportunities. Even more useful, because they are not involved in genetics, are molecules that play a precise role in cell metabolism. One example is a protein (cytochrome c) that plays a well-defined part in the electron-transport chain in all aerobic organisms. Small changes through mutation can upset this vital function, so cytochrome is conservative in terms of molecular evolution. The DNA in mitochondria plays no part in the combining of genes and mutations through the sex lives of eukaryotes, and so mitochondrial or mtDNA is likely to be more conservative than nuclear DNA. Ribosomal RNA (rRNA) performs the same assembly-line function in both eu- and prokaryotes, and it too is conservative. Such conservative molecules, though affected by genetics, have slow rates of change but contain many neutral mutations. They are the most important sources for studying relatedness and hold out possibilities for absolute dating of relatively young divergences. Since rRNA is common to both pro- and eukaryotes, it has been a molecule of choice for charting universal relatedness. This began with the work of Carl Woese in the 1970s. However, as the speed of sequencing of DNA increased exponentially since Woese had begun to piece together Darwin’s notion of a Tree of Life, the focus has steadily shifted to using DNA. By 2015, of the approximately 1.8 million named species of organism about 410 thousand (22%) had archived DNA sequences accessible via the Internet. Assessing relatedness between this diverse host of living organisms is now possible. But a look at the earlier developments is most instructive.
Roots of the family tree
By charting rRNA sequences, molecular biologists soon had a big surprise. What had previously been thought to be merely oddball bacteria that survived in inhospitable places, to which they might have adapted by geologically late evolution – the methanogens and sulphobacteria – turned out to be as fundamentally different from other bacteria as they in turn are from the eukaryotes. This discovery lay at the root of the 3-fold scheme for a universal division of terrestrial life into archaea, bacteria and eukarya. It implied that such a division had arisen very early in life’s history.
The tentative, early linkages among pro- and eukaryotes appear in Figure 14.1, where the distances between branchings express molecular differences in rRNA. Distinctions among the metazoa – plants, fungi, animals and us – cannot be resolved at the scale shown. Up to now, absolute geological timing of genetic branchings based on any genetic material has proved elusive, but Figure 14.1 shows conclusively that the bacteria, archaea and eukarya formed separate groupings a very long time back. The nature of the barrier to turning a tree of relationships into a clock is not hard to guess. Scientists must judge the rate of mutation from well-dated fossil evidence for the divergence time between groups that have clearly recognizable, living descendants. Only groups whose relatedness can be established from fossilised parts and for which fossils are known in dateable rocks can provide means of calibration. So only metazoans that secrete hard parts are candidates, as single cells in rocks can not be reliably distinguished. Absolute dating of divergences has been possible to a limited extent for primates and long-separated groups of modern humans, and also for some of the major groups of plants and animals, but the limit is not much more than 600 Ma ago. For the 3-fold divergence of all living things there are no reliable fossils. Tantalizing as Figure 14.1 is, at best it gave just a glimpse of the relative ages of major molecular events. Taken at face value, the rRNA results suggest that the bacteria and archaea diverged first. Then the molecular thread leading to the eukarya separated from the archaea.
Figure 14.1 An early evolutionary tree based on rRNA that links the three living domains, the bacteria, archaea and eukarya. Distances on the tree represent degrees of difference between rRNA sequences for some examples from each domain. Bold lines represent prokaryote groups that live in extremely hot environments.
Comparative biochemistry can only support an early divergence of the three fundamental domains from an ancestral line, leaving the descent of eukaryotes from the archaea as an open question. The common stock for all three molecular domains must have been some kind of primitive prokaryote. The similarities in cell architecture of the bacteria and archaea, their great differences from the cells of the eukarya, and the distinct possibility that eukaryan cells assembled by endosymbiosis between prokaryotes strongly support that notion. Just what the common ancestor of the three molecular domains was, what it did and where it evolved are, to say the least, debatable issues. Yet is has been given a name; the last universal common ancestor or LUCA Fortunately living descendants of the earliest branchings offer some hope of unravelling the last issue.
The most primitive bacteria and archaea use several metabolic chemistries, but all now live in hot places. They are thermophiles that have optimum growth at temperatures exceeding 80°C. The simplest view is that their ancestors, and their last common ancestor at the first branching in the divergence were thermophilic too. Tempering this is the alternative that during the whole of biological evolution tiny changes in genes may have allowed adaptation to life in the hot lane. We are entering speculative realms. To retain more caution, bear in mind that the rRNA thread guessed to represent the source of the present 3-domain molecular division could have been one of several early ones and several types of environment, both cool and hot. Whatever, it was the only one to survive to the present.
There are two views of this single, root stock of heat lovers. First, it and only it arose in hot places, of which the Earth has only one set of candidates that have been present since the Hadean – those near to volcanic vents. Water is essential for life, and so hydrothermal systems in the early oceans form the focal point for one set of views on the origin or early survival of life. Even in the deepest oceans, devoid of light, bacterial communities today thrive in black smokers. The second view is that only primitive organisms equipped for hot water would have survived the massive bombardment of the Earth that took place between 4.1 and 3.8 Ga ago. Impacts as large as those predicted in Part III would indeed have raised ocean temperatures, perhaps even to boiling point. The most likely haven would have been in the cooler depths, where only chemo-autotrophy would have been an option for the base of the primitive food chain.
There is some non-genetic molecular support for this view. Proteins that include iron and sulphur, and several other metals that are only abundant in lavas and hydrothermal fluids, take part in crucial life processes in all three domains; a persuasive example is Rubisco, the most common enzyme on Earth and centred on an Fe-S bond. Another prop for a heat-loving, last-common ancestor is the presence in many modern cells of proteins that help other protein chains to fold in a wide variety of processes, including photosynthesis. One of their roles is to repair heat damage; they are generally termed heat-shock proteins, despite their many other functions. One last point about thermophiles, for the moment; at least one such member of the archaea, Sulpholobus, can exchange genes from individual to individual. That trick is at the centre of the success of the eukarya, being fundamentally what happens in sexual reproduction. It is also a process that may have been passed on to the bacteria and, incidentally, is a major factor behind the plague of drug-resistant pathogens that challenges both health services and pharmacists.
Margulis’ theory of an endosymbiotic origin for the cell architecture of the eukarya (Figure 12.8) demands a look at the molecular contents of chloroplasts and mitochondria. Both can multiply by simple binary fission or cloning, as do all prokaryotes, and they contain DNA that is different from that in the cell nucleus, both in base sequences and in form; part of their molecular evolution lies outside that of whatever formed the eukaryote nucleus. Mitochondrial DNA is also in closed loops, as in prokaryotes. However, the mitochondrial DNA molecules are much shorter than those in the nucleus, and code for only about 10% of the proteins in organelles. Mitochondria and chloroplasts have partial genetic autonomy, but must have lost genes to nuclear DNA. That is why they cannot live outside of the cell. Is this evidence for a prokaryote facility to randomly exchange genes? If it is, then comparing organelle DNA or rRNA sequences in living prokaryotes is fraught with problems. The evolutionary advance of one group may somehow have been ‘grafted’ onto another. Again, the message is, ‘Proceed with caution’.
Sequences of rRNA in both mitochondria and chloroplasts bear more resemblance to those of bacteria than they do to either those in archaea or in the cytoplasm of eukaryote cells. Comparing the DNA of the three domains, that in the cytoplasm for the bacteria and archaea and that in the nucleus of the eukarya, is difficult, but it reveals an intriguing feature. The DNA from eukarya and archaea is full of junk sections or introns that have to be cut out when messenger RNA is produced. The DNA of bacteria is more streamlined and contains few if any introns. Here are two measures of support for Margulis’ lateral thinking about endosymbiosis. Suppose,. For the moment, that the clutter of introns in the DNA of archaea and eukarya demonstrates that the first eukaryote cell formed from a primitive member of the archaea. That began a relationship with a member of the bacteria, maybe a whole gang of them. To become endosymbionts they would have to get inside the existing primitive cell. Nearly all cells of all kinds are held together by both a cell membrane and a cell wall; a double protection. For something so tiny as a cell, this is hard to breach. The most likely host for endosymbionts would have to be a sort of floppy, wimpish prokaryote. As it happens (!) there is such a thing today. Thermoplasma, a denizen of hot, acid coal heaps, has no cell wall. Though it is not so primitive as some members of the archaea, it is a thermophile. Thermoplasma is also unique among the archaea, and has DNA that is associated with proteins related to those called histones, which bind DNA in the eukarya. This strange organism may be descended from the founder of the evolutionary line that exploded to end up with ourselves; a life-form so challenged by the rest of the world it could only survive some ancient threat by taking in lodgers.
Mitochondria were the first endosymbionts, if Margulis is to be believed. The most similar living things to mitochondria, as far as rRNA sequences go, are purple bacteria. They are a mixed bag and include chemo-autotrophy, anaerobic photo-autotrophy and aerobic respiration in their metabolic repertoire. The last lifestyle is what the vast majority of the eukarya enjoy, and mitochondria provide ATP, fatty acids and NADH in order that life can go on. Chloroplasts enable plants and single-celled algae to photosynthesise. Their rRNA is generally most similar to that of blue-green bacteria. However, detailed molecular studies of chloroplasts across the whole range of photosynthesisizing eukarya shows that taking in photo-autotrophic symbionts was a popular strategy for a long time; having a built in food synthesiser is handy. Red algae took in blue-greens, and so did green algae and land plants, but the other five main lines of algae emerged by taking in other eukaryotes.
If all this looks a little too convenient, it is worth bearing in mind that all sorts of symbiotic relationships among prokaryotes might have arisen, but only a few of many possible early lines of complex cell survived to the present. Their ancestors had a general fitness as regards the changing environment, and we shall now go on to how organisms might have influenced the environment and, through it, life’s subsequent course. We have a snowball in Hell’s chance of learning of other developments that failed to pass the test of natural selection. But before proceeding, Figure 14.2 is a graphic representation of the degree of relatedness of all 2.3 million named species from every division of modern organisms, which is based on several tens of thousand trees of taxonomic relatedness covering all species, and genetic sequences for about 5 percent of them. An estimate of the total number of living species is around 8.7 million, and some 15 thousand new species are discovered each year.
The central part of this ‘Circle of Life’ shows branchings and lines of descent from the last universal common ancestor (LUCA) of all life as we know it. The closer to the centre a branching is, the older the evolutionary division that it represents. The adjacent ring is colour-coded to represent all the broadest taxonomic groups that exist today, the outermost ring representing the estimated proportions of the number of living species in each grouping. Note that the oldest branchings are mainly those between different taxonomic divisions and are arranged in a clockwise spiral according to decreasing relative age. Thus, archaea and bacteria represent the first evolutionary split from the notional LUCA; they then split from branchings that led to SARs (a mixed eukaryan group) , early algae and plants; then we see the division leading to fungi followed by a succession among metazoan animal groups, of which apparently ancestral arthropods were the last to diverge. Note the relatively early branching of the deuterostomes, to which we belong, from ancestors of the most primitive metazoans, of which more later. By way of a little more explanation: SARs include diatoms, foraminfera, amoeba and brown algae; archaeplastids are green and red algae; early metazoans include cnidaria (corals, jellyfish and others), comb jellies and sponges; deuterostomes cover vertebrates, echinoids and some worms; lophotrochozoa contain molluscs, brachiopods and segmented worms; nematodes are roundworms; arthropods are made up of insects, crustacean. and spiders.
Figure 14.2 The ‘Circle of Life’ as compiled by Cody Hinchliffe of the University of Michigan and 21 collaborators from the USA, and partly based on Fischetti (2016). Increasing closeness of the ‘splits’ to LUCA suggests increasing relative age.
Despite looking a great deal more impressive than early attempts at using mainly RNA to sneak up on LUCA to (Figure 14.1), fundamentally it shows the same conclusion; neither archaea nor bacteria can be distinguished as the oldest descendants of the last universal common ancestor.
Between the rock and a hot place
The molecular evidence from all life that survives points strongly towards a source around hydrothermal vents in the deep oceans. Was that the environment where life first began or was it the only haven from the crescendo of bombardment that immediately preceded the first isotopic evidence for living processes? The simplest approach is to assume life originated where sulphides, clays and maybe zeolites formed abundant templates for the building of complex molecules en route to RNA and DNA, and where ferrous iron and alteration of igneous silicates provided reducing conditions. Yes, hydrothermal vents are the best bet, given all the evidence. Life was first a prisoner of chemistry, ultimately the chemical disequibrium between water and volcanic lava. Chemo-autotrophy is a simple life, but such are the possibilities outlined in Chapter 12 that it can be an extraordinarily diverse one, albeit taking only the form of slimy biofilms and mats. That diversity is reflected by the wealth of oddities among the heat-loving archaea and bacteria that still survive. But it is a life hovering between the ‘frying pan and the fire’. Dark as a submarine vent environment might appear, it is bathed in long-wave radiation emitted by hot lava. Prevented from boiling by high pressure, hydrothermal plumes can be edged by temperature gradients of up to 400°C over a matter of a few centimetres. Being water-based, living cells absorb that radiant energy and must die if too much gets in or if they stray into a plume. Yet just such a dangerous environment provides abundance in terms of its highly varied reducing and oxidizing conditions – availability and exchange of electrons and H+ ions. Euan Nisbet of the University of London sees this knife-edge as a driving mechanism for early evolution towards different life styles.
Organisms that depend on hydrothermal chemistry and heat face two risks, starvation if they move away from the plume or cooking and perhaps poisoning should they move too close. An insurance policy combines a means of detecting radiation, one of moving in response to its intensity and some kind of repair kit. The last are the heat-shock proteins, now adapted throughout living cells for their property of conferring folding on other proteins. A heat detector, essentially a mechanism tuned to critical wavelengths of radiation, must produce some output signal that other cell functions respond to. It must produce electrons, for electron transfers are involved in all signalling at the cell level. But electrons have implications for the proton pumping involved in cell metabolism. A radiation detector is not a nanometre away from a power source; it is one. The photosynthesizing pigments of some surface-dwelling bacteria (purple-sulphur and green bacteria) respond to infrared rays just beyond the visible range that are available in solar radiation (Figure 12.3). Their operating wavelength ranges are the only ones of those emitted by temperatures around 400°C that water will transmit. This intriguing coincidence suggests that heat detection by a thermophilic ancestor may eventually have been transformed to photo-autotrophic use, thereby opening up a new environment freed from the dangers of hydrothermal life. Permitted to use part of sunlight, such early phosynthesisers would then have faced the hazard of ultraviolet radiation, rampant in an oxygen- and therefore ozone-poor atmosphere. But these are not freewheeling organisms, they use light but depend on other chemistry (mainly using hydrogen sulphide – Figure 12.4) to maintain their electron flow. They demand an environment that is chemically reactive in an inorganic sense. To truly break out from chemo-autotrophy required exploiting water itself as a source of electrons for cell processes.
Planck’s Law shows that the energy carried by photons of electromagnetic radiation is directly proportional to the radiation’s frequency (i.e. inversely proportional to its wavelength). As I briefly explained in Chapter 12, extracting electrons from water demands exploiting the photon energy of visible light. To use them requires a powerful reducing agent. Both requirements are combined in the pigments of blue-green bacteria. Closely associated with one (chlorophyll) through the Calvin cycle is a protein based on the Fe-S bond – the all-powerful enabler of most of modern life, Rubisco. Having evolved radiation sensors cum power sources, they in turn form a plank to full photosynthesis by adjusting to the dominant wavelengths of radiation at the surface. Nisbet sees Rubisco itself as a chemical descendent of heat shock proteins by much the same general progression from a necessity becoming the ‘mother of all inventions’. It all seems so – well – inevitable. Life’s origin (or early survival) in a chemically rich but extreme environment lays down essential processes at the cell level that form the basis for adaptation to more widespread and less-severe environments. From the dark dangers and delights of exclusive and catholic chemistry ‘clubs’ around isolated sea-floor vents to the ultimate in seemingly free lunches, the ocean surface bathed in sunlight. But there was a price to pay.
Extracting electrons from water so it might combine directly with CO2 to form carbohydrate, frees oxygen from H2O (Equation 3.1), and that is deadly to a life function centred on reduction. Fortunately our diet and that of all animals, and the make up of all organisms that produce oxygen or inhabit oxygenated places contain antidotes that now find their place on pharmacy shelves – the anti-oxidants, of which beta-carotene is one. Many of these are light-harvesting pigments bound up in autotrophic bacteria and eukaryotes with chlorophyll-based photosynthesis, but absorb in the ultraviolet to blue end of the spectrum rather than blue and red light. They have a dual potential, defending against both oxygen toxicity and UV damage. The last must be primitive since free oxygen inevitably yields ozone when exposed to UV, which, in turn, confers atmospheric protection from ultraviolet radiation. Perhaps anti-oxidants too are a legacy of early life at the margin.
The carbon isotope information from early sedimentary rocks (Figure 13.1) that suggests the influence of life processes as far back as 3.8 Ga ago is ambiguous. Some say that it indicates life based on Rubisco, possibly including photosynthesisers, but the very negative d13C values in the earliest part of the record are best matched by modern methanogens. The thermophilic nature of many methanogens or their close relatedness to thermophile archaea suggests that they may have arisen in hydrothermal environments. Carbon isotopes are good for demonstrating life’s existence in the early Archaean, but not for much else. Those ancient deposits also contain sediments that are unusually rich in iron oxides – the BIFs of Chapter 8 – whose precipitation presents a paradox: highly reduced ocean water able to contain dissolved ferrous iron yet a source of abundant oxygen before any manifested itself in air. The logical conclusion might seem to be this: most of the oceans were oxygen-free and contained dissolved Fe2+ yet where shallow enough for sunlight to penetrate to the seabed photosynthesisers that had evolved to emit oxygen. That in turn was consumed by the oxidation of ferrous to ferric iron, and locked inescapably in local BIFs. The paradox is deepened by the intricacy of BIFs’ fine banding, which seems more likely to have formed in deep water than shallow basins; incompatible with oxygenic photosynthesis. Moreover, data on iron isotopes and rare-earth elements from the Fe-rich layers suggested in 2009 that deposition was in oxygen-free water. Also, BIFs are not exclusively made of iron oxides, up to a half of their volume being silica in the form of flinty layers; as well as being Fe-rich, Archaean oceans probably contained extremely high amounts of dissolved SiO2. When examined closely the cherts turn out to be heaving with nanoparticles of iron silicates. Discoveries of stromatolites in BIFs as well as in ancient limestones, together with signs of filamentous microfossils in the delicate, sub-millimetre banding of younger BIFs help to resolve the paradox. By analogy with some rare iron-oxidizing modern autotrophs, BIFs may have precipitated biogenically in the absence of free oxygen.
Ferrous iron-rich ocean water cannot contain dissolved oxygen, so most living things in the Archaean occupied anoxic ecosystems; paradise for the oddly diverse biochemical strategies of the prokaryotes. The tree of relatedness (Figures 14.1 and 14.2) points to diversification of bacteria and archaea at a very early stage, to occupy the niches determined by chemical possibilities. Many strands that survive are chemo-autotrophs and there are non-oxygen producing photosynthesisers among surviving bacteria. One important group today, and probably even more dominant on the oxygen-free Archaean ocean floors, are those which generate methane, and thereby add to the ‘greenhouse’ effect. But primary production of carbohydrate created another wide ecological niche, that of heterotrophy. There are various anaerobic fermenters among both archaea and bacteria, including one candidate host for the endosymbiotic origin of the eukarya – the flabby Thermoplasma. Just as genetically primitive are aerobic heterotrophs, of which the halobacteria live now in extremely salty shallow water. They have a dual life style, partly photosynthesizing using a red pigment (green and blue absorbing). That pigment, bacteriorhodopsin, is closely similar to rhodopsin that is the light-sensitive basis of all sight among the animal kingdom of the eukarya. Creationists who dwell on the ‘impossibility’ of vision without divine intervention will no doubt ignore such a clear demonstration of the generation of ‘unforseen’ opportunity by the chemical side of evolution, and of its great antiquity.
So, Archaean times seem likely to have witnessed a chemical explosion of diversity, but it would have had two restrictions. No prokaryote can swim very far, so all niches were two-dimensional at the interface between lithosphere and hydrosphere. Secondly, it was believed until quite recently that there could hardly have been an explosive evolution, because prokaryotes seemed likely to exchange genetic material between individual cells rarely and irregularly. There was no sex, for prokaryote reproduction is by simple fission of cells and one-to-one replication of DNA loops. They clone. Teeth left unbrushed bear witness to the fearsome pace at which tiny prokaryotes reproduce to form dental plaque. Despite this, it used to be thought that the only genetic diversity that enters into a prokaryotic population is by chance mutation, with the following consequences. Whatever that confers, it is passed on willy nilly as a new part of otherwise exact copies of DNA. An unfavourable mutation is a curse on all descendants, with no means of escape. But with only about 5 million ACTG base pairs, the probability of mutation at any one site is pretty low for prokaryotes, around one in a billion for each replication. So an average of a thousand splits results in one mutation, favourable, neutral or disadvantageous. Potentially favourable mutations need a huge number of cloned generations before sufficient accumulate to confer increased fitness on all individual cells. Once achieved however, that success is locked in place in all succeeding generations of clones. Cloning with conservative accumulation of mutations seems a safe way of living. That view has changed starkly now that a rapidly increasing number of prokaryote genomes have been sequenced.
It turns out that prokaryotes readily exchange genetic fragments and even entire genomes between strains of the same species, from species to species and probably between genera by horizontal gene transfer. Such transfers lie behind the explosive emergence of drug-resistant bacteria and a great deal more that is beyond the scope of Stepping Stones. Through a kind of opportunistic genetic exchange, prokaryotes actually evolve at rates far beyond those which eukaryotes are capable of. This perhaps enabled them to survive, or evolve through, the perils of an increasingly oxygenated world. Their ecology and evolution enters into eukaryote metabolism in the most intimate ways as what could be termed ‘microbiomes’ – no eukaryote is free of prokaryotes within and on their surfaces in countless trillions, with ever-changing diversity and ecological relationships.
In the human gut alone the number of prokaryote genes outnumbers those in our own genome by more than a hundred times.
These mainly symbiotic roles and flexible relationships between prokaryotes and their individual genomes seem likely to have enabled the endosymbiotic origin of eukaryote cells (Chapter 12), which superficially dominate our perception of organic diversity. Both groups continually interact both biochemically and through horizontal gene transfer; a point worth bearing in mind when we consider the post-oxygenation evolution of tangible organisms based on the eukaryote framework. From about 650 Ma ago they left signs of their development as fossils, while their intimate, single-celled companions have left scant and contradictory traces.
Evolving an empire of sexuality
The origin of the eukarya, most likely by several different endosymbiotic relationships (see Figure 12.8), involved two things: most genetic material resides in chromosomes within a distinct, membrane-encased nucleus; cell divisions take two forms, one of which underpins sexual reproduction. Sex is very different from cloning and extremely successful, but that does not mean that it is entirely a ‘good thing’ in an evolutionary sense. For a start, at the level of complex multicelled eukaryotes, such as us, there are a thousand times more ATCG base pairs than in prokaryotes. As a result every replication has a commensurately higher chance of involving a mutation. Multicelled eukaryotes are especially prone to both advantageous and deleterious mutations. That poses threats and opportunities far beyond those in prokaryotes. The recombination of DNA from two individuals following the basic sexual process in which it splits into two single, spiral strands (meiosis) is effectively a shuffling of genes. It produces new combinations of base pairs that might only recur once in countless such repetitions. A harmful mutation does not doom all offspring, nor are all of them favoured by a mutation that confers advantages. The reflection in phenotypes, whether single or multi-celled, is one of uniqueness within similarity. This is explosive in the sense of the potential number of permutations of genes that are pitted against the world in the form of individuals and the ‘equipment’ at their disposal. Rather than being destined in prokaryotes to remain in the same genetic milieu until fortuitously joined by others that may trigger an evolutionary step, potentially favourable genetic mutations in eukaryotes continually move from assembly to assembly. Such mutations are therefore not hampered in playing a multi-gene evolutionary role by the baggage with which they arose (but the same goes for fatal combinations). For single-celled eukaryotes that reproduce at a pace little different from prokaryotes the huge advantage is clear. Even for the slower pace of reproduction by multicellular eukaryotes, in which individuals of different sexes are generally involved, such repeated deals from a very large deck still means more rapid evolution – speciation and extinction – than in the bacteria and archaea.
Pragmatically, sex is evolution’s biggest success story, but look a little deeper and more logically. Beyond our human experience (and that is a two-edged sword), sex can be pretty awful. After tearing wounds in the arms of females with their horny beaks and tentacle hooks male giant squid (Architeuthis) inject packets of sperm under high pressure into the lacerations. At their leisure, spawning females release the sperm packets by ripping off the skin that heals these lesions. Sex carries a more general price too. Energy must be expended, even in performing the curious dance of the chromosomes and the strange aukaryotic recombination of halved strands of DNA. We know full well that a great deal of human endeavour is devoted to tracking down a mate, with more failures than blissful union. And copulation is often a botched job in terms of productivity. Clones beget clones with little effort at all and this reproductive process seems best from a thermodynamic standpoint, and progeny is 100% guaranteed. Bound up with the advantages of recombination is the risk of gamblers’ ruin, for the same winning hand is never dealt again! Having won the jackpot, what is to stop the ‘female’ switching back to cloning to ensure lots of nice little daughters? Such females-only parthenogenesis (virgin-birth) is achieved naturally by many plants and even some toads, so it is still an option for eukaryotes. Some biologists fret because the rise of sex seems both unlikely and disadvantageous. It is neither the statistics nor the genes that are selected for in a Darwinian way, but the individuals in whose functions genes manifest themselves. The emergence of sexual reproduction probably followed that rule.
Any early endosymbiont that permitted handy prokaryotes to enter the evolving eukaryote cell and strike a metabolic deal faced the risk of something unwholesome getting in and being a parasite rather than a pal. Cell-sized parasites able to exchange genetic material with their host – as are many modern infectious prokaryotes – soon adapt through their own rapid reproduction to the host’s genetic make-up. Reproduction without sex spells parasitised doom to the whole species assembled in this way. Sexual reproduction allows recombination to keep ahead of a parasite’s potential for evolution. Musing on this throws up another deeper possibility. Maybe Margulis’ endosymbiotic precursors to mitochondria, chloroplasts etcetera were parasitic invaders, ‘tamed’ by the essential sexuality of the nucleus. That is leading us into yet more uncharted territory, for the nub of eukaryote origins and that of sex is the development of the cell nucleus with its DNA organised in chromosomes. No one has much of a clue about that, except that both aspects require unique structures in eukaryote cells that form a sort of structural bracing, or cytoskeleton, within the cell and its component parts. The cytoskeleton permits eukaryotes to engulf, and temporary skeletal elements known as microtubules are essential for the ‘engineering’ of both mitosis and meiosis. Endosymbiosis and sex go hand in hand, but cytoskeletons seem likely to be primary. Finding their source means either looking for ‘fossil’ cytoskeletons, or seeking traces among living organisms. Both require an optimism rivalling that among supporters of England’s national soccer team. As yet there is no consensus on how meiosis and sex arose. But there are three suggestions: inheritance; evolution and a mixture of both. Because the common intestinal parasite Giardia intestinalis, a simple eukaryotic protozoan, contains within its genome a set of genes that function in meiosis this may have been inherited from a common prokaryote ancestor of all eukarya. Mitosis involving splitting and recombination of nuclear DNA strands shares many features with meiosis, so perhaps meiosis evolved from mitosis within an ancestral eukaryote. But that begs the question of where mitosis arose, for it occurs only in eukaryote cells. Thirdly, maybe mitosis and meiosis evolved in parallel in the protracted transition from prokaryotes to eukaryotes. And, in any case, how did the eukaryote nucleus, where mitosis and meiosis occur, originate?
One view is that a bacteria was invaded by an archaea, akin to the methanogens, which eventually formed the nucleus. A second approach focuses on a group of now rare bacteria that have a nucleus-like structure, and a propensity to engulf large molecules, but as yet offers no case for DNA to enter that nucleus and end up in chromosomes. A third, more extreme model is that the nucleus arose from a viral infection of a prokaryote. For us the origins of the eukaryotes and their functionality are supremely important, but the lack of a convincing model based on the very attractive idea of endosymbiosis is frustrating.
For the sake of an escape from casuistry, consider these facts: single-celled eukaryotes can swim, having a tail-like flagellum; all of them either produce oxygen or depend on it. Self-movement opens up a three-dimensional world, at least in water. However, being oxygen demanding, our ultimate ancestor seems tied in his or her origins to wherever blue-green bacteria produced it. Photosynthetic algal eukaryotes, among the earliest of their ilk (Figure 14.2), use much the same chemistry and physics as blue-greens, indeed chloroplasts are most likely derived from cyanobacteria endosymbionts. The finger for a eukaryote nursery is pointing, perhaps unsteadily at present, towards stromatolite colonies produced cyanobacteria, which abound in Archaean and Proterozoic sedimentary sequences. Whatever, mobility, oxygenic photosynthesis and oxiditative heterotrophy would have spread life inevitably to the open ocean. Such spatial exploration was armed with the basic photosynthetic ability to split water into electrons, oxygen and hydrogen, and with proton pumping (Chapter 12) to directly exploit CO2 gas in making CH2O, carbohydrate. Still buffered by originally magmatic ferrous iron, the origin and spread of the early eukarya to the open oceans must have stoked up the production of oxygen. Whether precipitation of ferric compounds consumed it, or oxygen accumulated so fast that it drove most ferrous iron from ocean water, mattered little to the new member of the biological trinity. The disappearance of BIFs and the appearance of the first dry-land redbeds around 2.2 Ga (Chapter 8), mark a decisive shift in the Fe-O2 balance.
Production of magma in the mantle must slow on average with the gradual decay of heat-producing radio-isotopes, and so too the rate at which iron, among other elements, transfers to the surface environment. Inorganic forces underpin the fundamental Fe-O2 equilibrium. However, eukaryote activity probably pushed the balance towards free atmospheric oxygen at a faster pace. That recurrent ‘probably’ is by no means a stylistic hedging of bets here, for the fossil record does not present us with anything resembling a eukaryote until 2.1 Ga ago at the earliest, and convincingly only as late as 1.4 Ga. The trend to more oxygen would have resulted also in an increased drawdown of atmospheric CO2 in train with the increased ocean volume occupied by life. Dead tissue now rained down to the ocean floors, there to become a food source for the fermenters and other prokaryotes in the lightless, oxygen-free depths. Since their metabolism does not produce the starting materials of carbon dioxide and water, but only some methane that returns to the atmosphere, much of the biological richesse would end up as dead tissue in films of slime rapidly to be engulfed and buried by sediment. Burial of organic carbon would have been a powerful means of reducing atmospheric CO2. So too the precipitation of carbonate by mats of blue-green bacteria in well-lit shallow seas. How and why they did that, is best dealt with in Part VI, because it brings in another chemical element with a vital interplay between geology and biology that much later launched the revolution of which we form a thinking part.
Grypania is not impressive, just a flat, glossy carbonaceous spiral in later Precambrian sediments (Figure 14.3). But it is a fossil; being easily visible it was probably multicelled; the only multicellular life is eukaryan, and so the best bet is that Grypania was some kind of algal colony. Somewhere between the origin of the eukarya (that could have been at any time since 3.8 Ga) and the appearance of such simple fossils as Grypania, the metabolic consortia in eukaryan cells must have found evolutionary advantage in both clumping together and coordinating different metazoan functions from the same genotype. How and why DNA became capable of turning different aspects of cell function on and off, so to segregate different metazoan body parts, is another deep and vexing problem. It too was one of many decisive steps that opened up possibilities for future biological events that are central to Part VI.
The largely hidden world of the most ancient life did not evolve in isolation. It seems to have been enabled, or at least preserved from cometary extinction, by inorganic chemical diversity and activity at the interface between the oceanic lithosphere and hydrosphere where new lavas react vigorously with ocean water. It spread to shallow water when the use of photo-electric pigments that probably evolved to detect fatal radiation turned into a metabolic power source, which exploited the radiation so abundantly shed by the Sun. Planck’s Law and some quantum theory behind the strength of the water molecule explain why water, the most abundant material at the Earth’s surface, could become a source of electrons and protons for biological processes. The downside was a dangerously toxic substance, free oxygen. The presence of dissolved iron in Earth’s original waterworld staved off self-extinction. There is no separating inorganic from organic worlds, no unbreachable boundary separating life from the deep mantle. Life’s origin and growth in abundance, and the burial of incompletely oxidised dead tissue and carbonate by-products of the blue-greens drew down the main ‘greenhouse’ gas CO2. Life changed and modulated the early Earth’s climate. Part V changes the focus on this interplay towards the great inorganic forces within the Earth and their role in climate, not excluding life but putting it in a wider, geological perspective.
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