Universe a grand tour of modern science Phần 10 ppt

cited possible risks to human health and the environment. World Food Programme officials told them that what was good enough for 280 million Americans was good enough for them. To the question, ‘Who decides about transgenic crops?’ the answer seemed to be no one in particular. E For more about natural gene mobility, see Tree of life. A stagnant pool was a treat for Lynn Margulis when, as a young biologist at Boston University, she liked to descant on the little green bugs that can so quickly challenge human notions about how a nice pond should look. Her favourites included the blue-greens, often called algae but in fact bacteria, which have played an outstanding role in steering the course of life on the Earth. Margulis became the liveliest and most stubborn advocate of the idea that we are descended from bacteria-like creatures that clubbed together in the distant past. Others had toyed with this proposition, but she pushed it hard. In 1970 she published a book, Origin of Eukaryotic Cells, and she followed it in 1981 with Symbiosis in Cell Evolution. These are now seen as landmarks in 20th-century biology, and the keywords in their titles, eukaryotic and symbiosis, go to the core of the matter. You are the owner of eukaryotic cells. Each of the billions of microscopic units of which you’re built safeguards your genes of heredity within a nucleus, or karyon in Greek. So, in the grandest division of living things, into just two kinds, you belong to the eukarya. That groups you with other animals, with plants, with fungi, and with single-celled creatures called protoctists, represented by 250,000 species alive today and often ambiguous in nature. The other great bloc of living things, the prokarya, are all single-celled, and the genes just slop about within them. The earliest forms of life on the planet were all of that relatively simple kind, meaning bacteria and similar single-celled 681 tree of life organisms called archaea. They ruled the world alone for half its history, until the eukarya appeared. Symbiosis means living together. The proposition for which Margulis first marshalled all the available evidence is that small bacteria took up residence inside larger ones—inside archaea, one would say now—and so formed the ancestors of the eukarya. Instead of just digesting the intruders, the larger cells tolerated them as lodgers because they brought benefits. The outcome was the microscopic equivalent of mermaids or centaurs. ‘The human brain cells that conceived these creatures are themselves chimaeras,’ Margulis wrote with her son Dorion Sagan, ‘—no less fantastic mergers of several formerly independent kinds of prokaryotes that together co- evolved.’ Oval-shaped units inside your cells, called mitochondria, are power stations that use oxygen to generate chemical energy from nutrients. They look like bacteria, they carry sloppy genetic material of their own, and they reproduce like bacteria. The same is true of chloroplasts, small green entities found in the cells of the leaves of plants. They do the work of harvesting sunlight and using water and carbon dioxide to produce energy-rich molecules that sustain plant life and growth. I A recount of the kingdoms In the Margulis scenario, the ancestors of the mitochondria and chloroplasts were indeed bacteria that took up symbiotic residence inside other single-celled creatures. The mitochondrial forebears were bacteria that had learned to cope with oxygen. When that element first appeared unbound in the ancient sea it was deadly dangerous, like bleach poured into the bacterial–archaeal communities. So bacteria that were adapted to it could offer their hosts protection against oxygen and also the ability to exploit it in new ways of living. Blue-greens, formally called cyanobacteria, were the ancestors of the chloroplasts. In their separate, bacterial existence, they had hit upon the most powerful way of using sunlight to grow by. It involved splitting water and releasing oxygen, and so the blue-greens were probably responsible for the oxygen crisis. But this smart photosynthesis also conferred on the hosts the capacity to generate their own food supplies. Host cell plus mitochondria made the ancestors of fungi and of protoctists. The latter included some distinguished by their capacity for swimming about, which became the ancestors of the multicelled animals. Host cell plus mitochondria plus chloroplasts made single-celled algae, and among these were the forebears of the multicelled plants. 682 tree of life Aspects of the scenario are still debated. Especially uncertain is how all of these cells came to organize their cell nuclei, and how they perfected the eukaryotic kind of cell division used in multiplication, growth and sex. The origin of the capacity for movement in protozoa, and its possible survival in the swimming tails of sperm, is also controversial. The broad brushstrokes of the symbiosis story are nevertheless accepted now. Not just as a matter of taste, but by verification. The kinship of identifiable bacteria with mitochondria and chloroplasts is confirmed by similarities in their molecules. Fossil traces of early eukaryotes are very skimpy until 1200 million years ago, but the molecular clues suggest an origin around 2 billion years ago, at a time when free oxygen was becoming a major challenge to life. In 1859 Charles Darwin described a ‘great Tree of Life, which fills with its dead and broken branches the crust of the Earth, and covers the surface with its ever branching and beautiful ramifications’. He meant a family tree, such that all extinct and living species might be placed in their relative positions on its branches and twigs. As it was pictured in those days, the plant and animal kingdoms dominated the tree. The symbiosis theory redefines the main branches of the tree, with more kingdoms. Bacteria and archaea, sometimes lumped together as prokarya or monera, originate near the very base, when life began. Half-way up the tree, symbiosis introduces the peculiar and wonderful microbes called protoctists, which include the single-celled animal-like amoebas and plant-like algae. Other protoctists, with multifarious characters that are hard to classify, represent obvious experimentation with symbiosis. A boat-like microbe inhabiting the digestive tract of termites in Austr alia, and one of Margulis’ prime exhibits, has recruited some 300,000 wiggly bacteria to row in unison like galley slaves. Membership of the animal and plant kingdoms is, in this new tree, confined to multicelled creatures, so excluding amoebas and the other protoctists. The fungi, which include yeasts and moulds as well as mushrooms, get a kingdom of their own. They thus rank alongside the animals and plants, but are distinguished from them by their lack of embryos. Fungi are very important in decomposing dead plants and weathering the rocks. But in view of the diversity of protoctists, there is something odd about singling out the fungi for special status. What about the algae, which nowadays totally dominate life on most of the Earth’s surface—meaning the upper film of the wide oceans? I Bacterial sex and gene transfers As scientists trace the course of evolution more precisely than ever before, the more confused it becomes. To Darwin’s way of thinking, and for 100 years after 683 tree of life him, the branches and twigs of the evolutionary tree of life represented distinct lines of descent. If different branches traced back to common ancestors, those existed in the past, and after them the hereditary pathways were quite separate. That was supposedly guaranteed by the fact that any mating between different species was sterile. Organisms classified, g rouped and named, according to their similarities and differences, hung on the Darwinian tree of life like Christmas presents. Each was in its proper place, with its label in Latin attached. But a bacterial guest in a symbiotic cell introduces into its host an inheritance from a completely different part of the tree. No longer do genes flow exclusively along a branch. They can also travel sideways from branch to branch, like tinsel. Some scientists call this lateral, others horizontal gene transfer. Was gene transfer a rare event? If it concerned only the invention of cells of the modern eukaryotic kind, 2 billion years ago, it might be seen as a rare historical quirk. But even before Margulis proclaimed evolutionary symbiosis, contemporary gene transfers between different lineages had turned up in hospitals. After antibiotics came into medicine in the 1940s, doctors were appalled by how quickly str ains of harmful bacteria outwitted the miracle drugs. Pharmacologists are still in a non-stop race in which each new antibiotic soon meets resistant strains. Hospitals have become superbug factories where patients may die, if not by the infections themselves, then by toxic antibiotics given as a last resort. Human beings did not invent antibiotics. They are ancient poisons used in conflicts among microbes. In England during the Second World War, the pioneers of penicillin ther apy simply harvested the material from cultures of a well-armed mould. From the point of view of the bacteria, it was not an unprecedented challenge, and some already possessed genes that conferred resistance. Evolve or perish—and evolve the bacteria did, at a startling rate, by distributing the genes for antibiotic resistance like insurance salesmen. Genes can pass from one bacterium to another, and even to different str ains or species. In a primitive form of sexual behaviour, one bacterium simply injects genes into a neighbour. A virus invading one bacterium may pick up a gene there and carry it to another. Or a bacterium can simply graze on stray genes liberated from a dying cell. Nor are bacteria the only organisms open to gene transfers, by natural genetic engineering. In animals, a gene can be transcribed into an RNA virus, which does not even use the usual DNA in its genetic code, and then be translated back into DNA when the virus infects a new cell. Unhappily some genes transferred by this reverse tr anscription cause serious diseases. 684 tree of life While medical concerns multiplied with these discoveries, fundamental biology was in some disarray. A basic assumption had been that organisms resemble their parents. Any alterations in the genes occurred by mutation within an organism and were passed on by the normal processes of reproduction. Evolution supposedly accumulated changes in an ancestral lineage that was in principle, if not always in practice, clearly definable. The symbiotic origin of our cells, the genetically promiscuous bacteria, and reverse transcription too, showed these assumptions to be naı ¨ ve. How important have gene transfers been, in evolutionary history? The answer to that question had to wait until molecular biologists worked out the tree of life for themselves, and examined complete sets of genes—the genomes—of present- day animals, plants and microbes. Then they could begin to trace individual genes back to their origins. I Doing without fossils The notion that one could discover the course of evolution from molecules germinated around 1960. That was when Brian Hartley at the Laboratory of Molecular Biology in Cambridge noted that poisons analogous to military nerve gases blocked the action of a wide variety of active proteins—enzymes—besides those involved in the control of muscles by nerves, which were the prime target of the nerve agents. He suspected that the various proteins had a common genetic ancestry. X-ray analyses showed how various proteins were shaped, and confirmed the idea. For example, three enzymes involved in human digestion, trypsin, chymotrypsin and elastase, turned out to have very similar structures. Other scientists compared proteins serving the same function, but in different species. Richard Dickerson of Caltech studied cytochrome C, which occurs in all plants, animals and fungi as an enzyme for dealing with oxygen. To perform correctly, it must have the same properly shaped active region, built by a par ticular sequence of subunits, amino acids, in the protein chain. But non-critical parts of the molecule could vary, and Dickerson found that by counting the differences between one species and another he could tell how closely they were related. For example, compared with cytochrome C in pigs, the same enzyme in chicken differs in 9 amino acids, in tuna in 17, and in cauliflower in 47. This was supermarket evolution. Instead of hammering on chilly rock faces, or wandering across searing deserts in search of fossils, you could collect your specimens in a basket at a local shop. If you felt more energetic you could catch a passing moth or frog to extend the scope of the investigation. You could then begin to construct a tree of life from the variable molecules in living organisms. 685 tree of life It showed how long ago, relatively speaking, these and other species shared a common ancestor. Fossil-hunters were duly miffed. The molecular scientists needed their help to put dates on the tree of life. To know how many millions of years ago chicken and tuna had the same ancestor, you needed the evidence of fossils from rocks of dated ages. But Dickerson complained in 1972, ‘The zoologists who have the best command of information on dates have maintained a reserved scepticism towards the entire protein endeavour.’ Rates of change in chemical composition during evolution differ widely from molecule to molecule, depending on how crucial its composition is for its purpose. For example, the protein histone H4 varies five per cent of its components in 2500 million years, while fibrinopeptide changes 800 times faster. A new chapter in the molecular investigation of evolution opened in the mid-1970s, with comparisons between special nucleic acids that are present in the vital equipment of every living thing, from bacteria to whales. Ribosomes are machines used by cells to manufacture proteins, and they incorporate ribosomal ribonucleic acid, or rRNA. This became the material of choice for getting the big picture of molecular evolution. Its leading advocate, Carl Woese of Illinois, Urbana-Champaign, noted that it included slow-evolving and fast-evolving portions, so that one could investigate the entire story of life on Earth, or home in on recent details. One of the first successes was confirmation of the symbiotic origin of the cells of animals and plants. The oval mitochondria, the power stations in the cells, have their own ribosomes with private lineages that trace back, as predicted, to oxygen-handling bacteria. Similarly, the round green chloroplasts in plants have ribosomes akin to those of the blue-green cyanobacteria. But the general-purpose ribosomes in animal and plant cells are more like those of archaea, the simple creatures similar to, but now distinguished from, the bacteria. Evidently the large host cells that found room for the bacterial lodgers were from that domain. I Counting the transferred genes If the tree of life inferred from ribosomal ribonucleic acid is to be believed, then the history of other molecules in the same organisms should match it. This is not always the case. Analysts found that they obtained different trees for the bacteria and archaea depending on what molecular constituents they compared, from species to species. The only explanation was that genes for some of the molecules came in by transfers, either recently or in the distant past. Even the grand distinction between bacteria and archaea was compromised by discoveries of widespread exchanges of genes between them. 686 tree of life To make sense of the muddle, Carl Woese reflected on the universal ancestor, at the base of the tree of life. He visualized it, not as a discrete organism, but as a diverse community of very simple cells that survived and evolved as a biological unit. Rates of genetic mutation and gene transfer were very high at first, but gradually the evolutionary temperature dropped. ‘Over time,’ Woese wrote, ‘this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.’ By those he meant bacteria, archaea and eukarya. Gene exchanges were much less frequent later, he said, and ‘the evolutionary dynamic became that characteristic of modern cells.’ Increasing evidence nevertheless told of gene transfers between species continuing in recent evolution. When the complete genome of the gut bacterium Escherichia coli became available, Jeffrey Lawrence of Pittsburgh and Howard Ochman of Rochester looked for aliens. They reported that no less than 18 per cent of the bacterium’s genes had been acquired in at least 234 transfer events during the past 100 million years. These were not just miscellaneous acquisitions. They included the genes responsible for E. coli’s distinctive appetites for lactose and citrate. A heated debate broke out, among experts in molecular evolution. By 1999, Ford Doolittle of Dalhousie University in Canada was declaring the very concepts of species and their lineages to be obsolescent. The best one could do, he suggested, was to ask which genes have travelled together for how long, in which genomes, without being obliged to marshal the data in defence of particular evolutionary schemes. There might be new principles waiting to be discovered about how genes become distributed between genomes. Doolittle invited biologists to consider that organisms are either less or more than the sum of their genes, and ‘to rejoice in and explore, rather than regret or attempt to dismiss, the creative evolutionary role of lateral gene transfer.’ Although he cautioned that it would be rarer in animals and plants, some enthusiasts for the new picture were ready to cast doubt on the definition of species even in those kingdoms. Among the scientists who reacted angrily was Charles Kurland of Uppsala. He protested that ‘Nothing in science is more self- aggrandizing than the claim that ‘‘all that went before me is wrong’’.’ The importance of gene transfer in the evolution of microbes was no longer in doubt, but Doolittle had good reason to query its importance in animals and plants. These are multicelled creatures, with intricate bodily organizations that would be easily disrupted by intruding genes. The fact that animals and plants often reproduce sexually also puts up a high wall against alien genes, which will 687 tree of life be inherited in the normal way only if they get in among the genes carried by eggs or sperm. Rare events might nevertheless become significant over long time-scales. When drafts of the entire human genome became available in 2001, molecular evolutionists pounced on them. They were looking for alien genes that might have been introduced from bacteria during 500 million years of evolution in animals with backbones. An early claim was that bacteria introduced more than 200 of the human genes, but these were soon whittled down to about 40. Some investigators thought that those, too, might disappear from the list as comparisons with distant animal relatives continued. Even if the first figure had been correct, any influx of bacterial genes would have been very small, compared with the transfers between bacteria. In the light of such evidence, Doolittle and his colleagues noted that ‘Our multicellularity probably saved us from participating in the dirty business of lateral gene transfer so beloved by microbes.’ They chose as their battleground for demonstrating the importance of gene transfer the single-celled eukaryotes— fungi, yeasts and the multifarious protoctists, half-way up the tree of life. Thus, by the beginning of the 21st century, biologists had to consider contrasting modes of evolution during the history of life. At the base, and long since extinct, is the universal ancestor comprising a superorganism of ill-defined cells that swapped genes freely. At the top of the tree of life, robust branches of plant and animal families, genera and species preserve the most familiar features of Darwin’s picture, with just a small though persistent infection with transferred genes. The trunk of the tree, representing most of the history of life on Earth, has gone wobbly. Replacing the old hardwood is a tangled web of evolving microbes— bacteria, archaea and single-celled eukarya. It resembles the early superorganism in a continuing habit of swapping genes. But the trunk also shows prolonged persistence of clusters of genes in microbial types that foreshadow the more obvious lineages and branches of plant and animal evolution. The microbial mode of evolution continues to this day. A neutral umpire might therefore declare the outcome a draw, in the spat between the traditionalists and the gene-transfer revolutionaries. Backed by the evidence of the human genome, the first group preserved their cherished picture of evolution in respect of plants and animals. The revolutionaries nevertheless amassed ample evidence that microbial evolution is different in character and will require a new theory to comprehend it. Arguments are bound to continue at the interface, especially concerning the single-celled eukaryotes. Can they, with their highly organized cells, really be 688 tree of life as promiscuous as bacteria are? And to puzzle the scientists anew is mounting evidence of molecular heredity that bypasses the genes themselves. Whether that will further disfigure the tree of life remains to be seen. E For more about molecular changes over time, see Molecules evolving. For an important branch-point of the tree of life, see Cambrian explosion. For more about blue-greens, see Photosynthesis and Global enzymes. 689 tree of life W here mexico’s sonoran desert encroaches into Arizona, a volcanic plug makes the pointed peak of Baboquivari. It is the most sacred place of the Tohono O’odham Nation, formerly known as the Papagos Indians. The peak is the home of I’itoi the Creator, and it provides the axis around which the stars revolve. This Native American idea about Baboquivari is typical of traditional cosmologies worldwide. In 1969 it served as an object lesson for the astrophysicist Philip Mor rison, visiting Arizona from the Massachusetts Institute of Technology, when he ruefully acknowledged the triumph of the Big Bang theory of the Universe. ‘We shall for a generation or two hold on to the most naı ¨ ve cosmology,’ Morrison said. ‘And not unless a wiser, more experienced generation comes after us will we change it. Perhaps they will see that it, too, was a provincial preconception.’ Morrison was speaking in the aftermath of the discovery of the cosmic microwave background, announced in 1965. It told of a time when the whole of space was as hot as the Sun, and it falsified at least the pristine version of the Steady State theory that had appeared in 1948. This said that the Universe was infinite and unchanging, with new matter being continuously created to fill the growing gaps between the galaxies produced by the cosmic expansion. Don’t laugh. The most persistent advocate of the Steady State theory was Fred Hoyle at Cambridge, one of the smartest astrophysicists of the 20th century. Many of his colleagues, including Morrison himself, preferred the idea. When Science Service in Washington DC took a poll of experts in 1958, it found their beliefs almost equally divided between the Steady State and the Big Bang. They all nevertheless gave an emphatic No to the question, ‘Is a poll of this kind helpful to science?’ The faint hiss of cosmic microwaves, rather than any shift in personal preferences, boosted the idea that everything began in a creative detonation at some moment of time. It also put a wrapper around the sky. 690 [...]... museum There is a Dark Age of a billion years, or perhaps much less than that, between the microwave background and the appearance of the stars and galaxies Very distant objects are also hard to see But improved telescopes and surveying techniques are giving more and more information about what was going on 12–13 billion years ago The three-way linkages of space, time and the speed of light have the curious... Ba n g 698 A s h f a l l i n g f r o m t h e s k y and great waves leaping from the sea afflicted Europe’s first urban civilization, which was that of the Minoans on the island of Crete Their ordeals are dismaying to contemplate, because the same things are certain to happen again some time That is clear from the inexorable nature of the cause, which is nothing less than the gradual annihilation of. .. l c a n i c e x plo s i o n s the scale of a human lifetime But the threats of volcanic tsunamis and climatic chills hang over many other people living far from the scene Tsunamis are a complex story because earthquakes, seabed mudslides and the collapse of inactive volcanic structures in great landslides can all make waves, as well as eruptions in volcanoes rooted in the seabed The waves are barely... Four years elapsed before it was traced to the Katmai volcano at the south-west tip of Alaska’s mainland, where the remains of an event now rated at 6 on the explosivity scale provide a tourist attraction, in the Valley of Ten Thousand Smokes Contrast that delayed discovery with the detection in 1985 of hot rock nearing the surface of Lascar in the desert of Chile, by British geologists examining images... have been seen Far from it Some objects are too faint at a great distance Others are hidden behind thick dust clouds, near or far And for every star, galaxy and gas cloud that modern telescopes can register, probably ten times as much mass is in the form of so-called dark matter, the identity of which has still to be established Dante believed that beyond the stars, out of reach of mortal eyes, lay... Russia, and thence via the Aleutian Islands to Alaska 704 vo l c a n i c e x plo s i o n s Every day, more than 100 passenger aircraft on polar routes fly over this northern boundary of the Ring of Fire The top priority for the Alaska Volcano Observatory, based in Anchorage, is therefore to warn the aviation authorities of clouds of dust reaching the stratosphere They are not kind to jet engines, and... release, European Southern Observatory, 16 October 2002 Gebhart: quoted in press release, Space Telescope Science Institute, 17 September 2002 Cash and colleagues: W Cash et al., Nature, vol 407, pp 160–3, 2000 Valtaoja: personal communication, 2002 Brain images Landau: W.M Landau et al., Transactions of the American Neurological Association, vol 80, pp 125–9, 1955 Scandinavian researchers: N Lassen... uncreative for the Earth to form and human beings to appear The geological and biological details are not at issue here How our planet preserved liquid water for more than 4 billion years, and how its geochemistry, modulated by impacting comets and asteroids, facilitated the appearance of quick-witted land-dwelling animals—those are local improbabilities for planetary scientists and biologists to fret about... the same reason as the Aegean Sea In the Java Trench a narrow residue of ocean floor, between Asia on the one hand and Australia plus New Guinea on the other, is diving to destruction, in a prelude to another continental collision in 10 million years’ time Fly lengthwise above Java, parallel to the ocean trench, and you’ll see volcanic cones poking through the clouds with a regularity that looks almost... the Earth and humankind The cosmos is as large as it is because its expansion till now is an exact measure of the aeons it took for us to show up after the Big Bang, and to start looking at it The galaxies, stars, interstellar clouds and comets tell of the cosmic order that was needed to accumulate the stuff for making our planet and us So the Earth regains its core position, not navigationally speaking . fogbank, to have a more direct view of the Big Bang, appear in Gravitational waves and Cosmic rays. Material contents of the Universe are to be found in Dark matter, Black holes, Galaxies and Stars There is a Dark Age of a billion years, or perhaps much less than that, between the microwave background and the appearance of the stars and galaxies. Very distant objects are also hard to see told of a time when the whole of space was as hot as the Sun, and it falsified at least the pristine version of the Steady State theory that had appeared in 1948. This said that the Universe was