How viruses influence evolution.
Virolution by Frank Ryan
One – An Enigma from the World of Plagues
p9 “Elysia chlorotica is a beautiful leaf-shaped sea slug that inhabits the salt marshes of the eastern seaboard of the United States…”
p10- “Life for the hermaphroditic slug begins as the first warmth of spring rouses it from the torpor of winter. Only now will it lay its egg masses into the brackish water, where, a week or so later, they hatch out as larvae. The larvae spend the next few weeks swimming here and there in the planktonic layers of the coastal marshes, all the while searching for the green filaments of a single species of seaweed, the alga Vaucheria litorea, to which they home and firmly attach. Having found the right alga, they complete their metamorphosis to tiny slugs, when they immediately begin to feed, rasping through the algal walls and sucking out the contents of its cells. Vaucheira is a green alga, which, like the green leaves of trees, is packed with tiny bun-shaped organelles, known as chloroplasts, which capture the bountiful energy of sunlight. This process, known as photosynthesis, is fundamental to the cycles of life, enabling plants to convert sunlight into chemical energy that can be stored, and further shared, by the animals that feed on plants…
p10-11 “Photosynthesis began perhaps as long ago as 3 billion years, when some early bacteria, known as cyanobacteria from their blue-green colour, evolved on our exceedingly young, and volatile, planet. A good deal later, through the evolutionary process known as symbiosis, these pioneering photosynthetic microbes were incorporated into early nucleated life forms, formerly known as protozoa but today called protists, which became the forerunners of the green algae and plants.But the cyanobacterial forerunners never went away. They still thrive in the planktonic regions of the oceans, and their ancestral forms also survive, through somewhat whittled down in their genomes, within the tissues of algae and plants as the tiny cellular inclusions known as chloroplasts. All of Elysia‘s rasping and sucking are directed at these chloroplasts, which it somehow separates out from the other contents of the algal cells, before secreting them away into special cells lining its gut. Soon the gut expands, branching out into various tiny channels all over the body of the growing slug, so that the precious chloroplasts end up in a confluent layer immediately beneath its skin. Thus replete, the slug abandons its mouth to become exclusively solar-powered for the remainder of its life, deriving alll of the energy it needs from the algal chloroplasts, which, like a myriad fairy lights within its leaf-shaped body, have switched on the illumination and turned it green.”
p11-12 “However, we are far from done with the Elysian mystery. the ingested chloroplasts must now continue to gather the energy of sunlight throughout the slug’s life, and this in turn would normally rely on a continuous supply of proteins, which would be coded by the algal nucleus. How then, since the chloroplasts are no longer connected to the algal nucleus, do they continue to survive and function throughout the nine months of the slug’s day-to-day life?
“In fact…at some time during the previous evolution of Elysia chlorotica, key genes have been transferred from the nucleus of the alga to the nucleus of the slug. Much remains to be discovered about this natural genetic engineering, but there is gathering evidence that it is made possible by viruses that inhabit the slug’s nucleus and tissues. One very interesting discovery about these viruses is that they possess a special chemical the enzyme known as reverse transcriptase, which usually tells us that we are dealing with a retrovirus. .. reverse transcriptase enables a retrovirus to invade the nucleus.
p12-13 “At the end of the slug’s life cycle, when spring is stirring the torpid animals back to life, and soon after the eggs for the future generation have been laid, the adult slugs begin to sicken and die. All of a sudden the viruses that previously appeared innocuous now teem and swarm throughout its tissues and organs. This is no chance observation since viruses are found to be multiplying in every dying slug, and virulent pathological changes throughout the tissues would point to an aggressive viral attack. These viruses are not invaders coming in out of the oceans since exactly the same pattern is seen in slugs that have been maintained in aquaria, in artificial sea water. It is hard to draw any conclusion other than that this attack is brought about by the very retroviruses that appear to inhabit the slug’s own genetic make-up, those same enigmatic viruses that enabled the genetic transfer of the chloroplast genes from the alga, and made possible the solar-powered life cycle. If so we appear to be witnessing a programmed annihilation of hte entire adult population as if the viruses that had previously enabled the slug’s somewhat idyllic life cycle had now switched behaviour and were acting out some more brutal pattern of programming culling the now-redundant adults after they had laid the eggs for the start of a new generation.
“If the circumstantial evidence is indeed correct, we are looking at an illuminating example of a powerful evolutionary mechanism known as “aggressive symbiosis”.”
Two – A Crisis of Darwinism
Three – the Genetic Web of Life
Sit down before fact as a little child, be prepared to give up every preconceived notion, follow humbly wherever and to whatever abysses nature leads, or you shall learn nothing. –Thomas Henry Huxley
p61-2 “It was clear, from lichens, that the traditional idea of parisitism was inadequate to explain the real complexity of what studies were now revealing of the very close interdependency of the fungi and algae that made up the diverse group. Other examples of intimate interdependency of different life forms were duly recognised, from the coral reefs to forest oaks. In time the German botanist, Albert Bernhard Frank, would discover that virtually every plant was in partnership with a variety of fungi that fed into ti, often physically invading the roots, so much so that the familiar root ball we shake out of its pot from the garden centre is largely fungus. The plant above ground supplies carbon compounds and energy to the fungus, while the fungus feeds water and minerals into the root. “
Four – the AIDS Dimension
Five – the Paradoxof the Human Genome
p125-6 “…we can learn a lot about the actual mechanics of such genomic unions if we examine another major symbiogenetic union that helped to construct the human genome – the ancient evolutionary event that gave rise to the mitochondria that enable us to breathe oxygen.
In the words of Lewis Thomas,
we are shared, rented, occupied. At the interior of our cells, driving them, providing the energy that sends us out for the improvement of each shining day [are the hundreds, or thousands, that] in a strict sense are not ours [within the cytoplasm – the part of the cell that lies outside the nucleus.
Most biologists now accept the evolutionary explanation, first advanced by Margulis in the late 1960s, that these were once oxygen-breathing bacteria that entered into a holobiontic union, more than a billion years ago, with a single-celled nucleated protist (formerly called a protozoan) that was the common ancestor of all the animals, plants, fungi and oxygen-breathing protists that populate the Earth today…
“The mitochondrial genome is made up of typical bacterial genes which, unlike our nuclear genes, are gathered together in the typical bacterial ring. They reproduce, independently of the nucleus, by the typical bacterial process of budding. In fact, as many people will know, the mitochondria are part of the cytoplasmic inheritance of the maternal ovum, so they are inherited exclusively from the mother, and the genomes of the mitochondria of all present-day life forms are so closely related in their genetic sequences that they could only have originated from a single ancestor. Remarkably, sequence analysis suggests that perhaps the closest known modern relative to the ancestor of all mitochondria is the bacterium, Rickettsia prowazeki, which causes one of the most notorious plagues of history, the louse-borne epidemic typhus.”
“If we now examine how natural selection has worked on the bacterial genome of our mitochondria, during its billion-year holobiontic evolution with nucleated life forms, we discover that the original genome has been radically changed and broken down. A great many of the original bacterial genes have been jettisoned – the ultimate silencing of unwanted components – meanwhile, some 300 or so genes have been transferred out of the mitochondria and into the nucleus, where, in a manner reminiscent of what we saw with Elysia chlorotica and its ingested symbiotic chloroplasts, these nuclear genes continue to work in a precise cooperation with the remaining genes in the mitochondria. One of the wonders of mitochondrial genetics is that , from a symbiotic union dating back roughly a billion years, the mitochondrial genes retain their quintessential bacterial nature. Indeed, as we shall see in a later chapter, this symbiotic origin of our human mitochondria has major implications for the genetics of mitochondrial disease.”
p129 “[Luis] Villereal believes that LINEs and SINEs, which together make up 34% of the genome, are retroviral derived or controlled These conclusions are staggering. They imply that viruses, and their closely related products, make up at least 43% of the known human genome – and as time goes by, and more of the unknown component of the genome becomes deciphered, this proportion is likely to increase.”
Six – How Viruses Helped Make Us Human
p132-3 “My continuing focus was how the symbiotic perspective extrapolated to the viral contribution to the human genome. From a Darwinian perspective, our human endogenous retroviruses are seen to be parasitic invaders. They serve no purpose, other than that of their own selfish evolutionary trajectory. I would not contradict the fact that virus-host interactions often begin in this way. It also seems reasonable to anticipate that some viral elements, even though deeply embedded in the genome, will still be subject to selection operating at selfish individual level. My intention is not to contradict Modern Darwinian evolutionary mechanics – I consider myself a Darwinian as well as a symbiologist. But I would nevertheless propose that we cannot possibly interpret the massive viral presence in the human genome if we fail to consider both perspectives. And I accept that during the first clash of interaction, when a retrovirus first invades a virgin host, the predominant evolutionary dynamic will be individual and selfish. But the dynamics change quite early in the partnership, especially when the interaction involves a pesisting virus. Here the two phases of aggressive symbiosis must also be considered an integral part of the evolving dynamic. Long-term viral survival becomes dependent on survival of a key subgroup of the original host – the surviving rudiment – which has itself been selected fro long-term partnership with the virus. In such circumstances a new evolutionary dynamic enters the picture: an ongoing symbiosis of virus and host in which selection will operate at the level of partnership.”
p134-5 “As far as I am aware, no genome has been more extensively colonised with retroviruses than our own human genome. I accept that the Modern Darwinian interpretation must apply, to a significant degree, to this vast viral legacy. It is nevertheless my contention that a significant proportion is also symbiotic, implying that we humans are, to an important degree, a holobiontic union of vertebrate and viral inheritance.”
p138-9 “[in the late 60s and early 70s] the discovery of viral genes being incorporated into host genomes was hard for contemporary scientists to swallow. In the words of the pioneer of the chicken viruses, Robin A Weiss
the notion of Mendelian transmission of integrated genomes of RNA tumour viruses in the germ line of healthy animals was regarded as bizarre.
“When Weiss, then working at University College London, submitted a paper demonstrating how a “normal” chick cell, which had a virus known as the avian leukosis virus endogenised within its genome, could pass on the viral coding for its env gene to another virus, thereby reviving the latter’s infectivity, the manuscript was roundly rejected, with one reviewer pronouncing that such a scenario was impossible. It was a powerful example of the a ability of viruses to surprise us with the complexity of their behaviour, as well as a warning not to treat viral genes and sequences as if they were the same as vertebrate genes and sequences, even long after holobiontic incorporation.”
Seven – the Implications for Medicine
But it is illusion to think that there is anything fragile about the earth; surely this is the toughest membrane imaginable in the universe, opaque to probability, impermeable to death. We are the delicate part, transient and vulnerable as cilia. — Lewis Thomas
Eight – the Autoimmune Diseases
p187 “In 2009 Luis Villarreal published a major overview of the origins of our adaptive immunity, in which he examined the interaction between viruses and hosts over the whole of the evolutionary time frame, beginning with bacteria, and moving through the earliest animals, such as the invertebrates, with their fixed but still reasonably effective systems of immunity, to the origins of adaptive immunity in the vertebrates, further modified with the origins of the mammals, then the primates, including humanity. The title was ‘The source of self: genetic parasites and the origin of adaptive immunity‘ and in his review he makes a cogent argument for the origin of a primal form of immune identity, and thus the first real establishment of the concept of “self”, through complex evolutionary interactions between phage viruses and their host bacteria.”
Nine – Cancer
The unfolding of events in the life cycle of an organism exhibits an admirable regularity and orderliness, unrivalled by anything we meet with in inanimate matter. We find it controlled by a supremely well ordered group of atoms… –Erwin Shrodinger
Ten – the Wider Dimension
p230-1 “The subject of [Lynn Margulis, founding figure of modern symbiology's] keynote speech was the origin of the first nucleated life forms during the Proterozoic aeon, more than two billion years ago, during the early evolution of the biosphere, a time when there was no oxygen in the atmosphere. Here, according to Margulis’s serial endosymbiosis theory, or SET, the first nucleated cells evolved from the fusion of two bacteria-like cells, one possibly a fast-swimming sulphur-loving bacterium coiled like a corkscrew – a spirochaete rather lie the bacterium that causes syphilis today – and the other an archaebacterium which some would call an Archea, similar to the organisms that live in the hot springs of Yellowstone Park today. This fed, in a metabolic symbiosis, off the hydrogen sulphide produced by the spirochaete. In time the fusion of these two organisms led to the first unicellular nucleated life forms.
“Later, with the evolution of the first blue-green cyanobacteria, around the shorelines – the forerunners of the chloroplasts in today’s algae and plants – we had a life form that could capture the energy of sunlight and produce oxygen as a by-product. In time, this would change the atmosphere to what we know on Earth today. Then, more than a billion years ago, an oxygen-breathing bacterium, the precursor of mitochondria, joined the growing holobiontic union to give rise to life as we see it today, the animals and plants, fungi and some of the protists.”
p233 “When [Marilyn Roossinck] spoke she took us all by surprise, describing how she had pioneered a new experiment, based on symbiological methodology, to search for hitherto unknown viruses in nature. She had, almost immediately, discovered a virus symbiotic to plants growing in the arid ecology of Yellowstone National Park. The virus infected a fungus which itself infected a tropical panic grass that grew in the geothermal soil. The fungus was known to confer heat tolerance on the plant a familiar pattern of symbiosis. But when she “cured” fungal isolates of their “infecting” virus, the plants containing the fungi were unable to withstand the arid heat and they died, just like plants with no fungus at all. When she reintroduced the virus the to the fungus it restored the heat tolerance of the grass Subsequent research by Roossinck and her associates suggests that the virus may be contributing a metabolite that enables the survival of the three-way symbiosis.
“It was a pioneering discovery, spectacular enough to ensure her subsequent paper, with the title, ‘A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance‘, would subsequently be published in the prestigious American biology journal, Science.“
p239-40 “Michael Syvanen … recapitulated the evidence he had gathered from whole genomic analysis of phyla about the evolutionary period, known as the Cambrian Explosion – which is one of the greatest enigmas that currently faces biology – during which, over what appears to have been a relatively brief period of perhaps 20 to 40 million years, all but one of the great animal divisions appeared in the fossil record. Syvanen had a hypothesis to explain the enigma. In his words,
When I first started thinking about the evolutionary implications of horizontal gene transfer, it seemed quite natural to suggest that gene transfer between phyla could explain the phenomena of both the speed and observed parallelisms of the Cambrian radiation.
“If this explanation were correct, then there should be evidence for such transfers in the genomic sequences of the various phyla. But when he examined the evidence, he found that the genomes of the sea urchin and the humans fitted into a common clade, which excluded the phylum of tunicates. though it may seem obscure to lay readers this contradicted conventional thinking on the basic trunks of the evolutionary tree of life, which placed the tunicates and vertebrates (including humans) into one of the basic trunks that included the chordate phylum, while it placed the echinoderms, including sea urchins, in the other. He wondered if he was witnessing the genetic signature of something quite remarkable: a gargantuan genetic transfer long ago – possibly through hybridisation between two wholly different phyla.”
Eleven – Sex in the Evolutionary Tree
p266-7 “Today we recognise that many groups of animals include hybrids, including the dzo, zo or yakow, which is a cross between a domestic bull or cow and a yak; the beefalo, which is a cross between an American bison and a domestic cow; the liger, which is a cross between a lion and a tiger; the wholpin, which is a cross between a false killer whale and a bottlenose dolphin; and the Wurdmann’s heron, which is a cross between a white and a great blue heron. Other crosses include the albino king snake and albino corn snake, the Galapagos finches, canine hybrids between coyotes, wolves, dingoes, jackals and domestic dogs, crosses between various species of deer, and between a polar and a grizzly bear.
“Environmentalists and conservationists are now conserving not merely species but also evolved genes. The greater the genetic diversity the more likely ecosystems will survive. And hybridisation is increasingly recognised as one of the ways in which ecosystems embrace, and preserve, genetic diversity. For example, Brad White, a wildlife geneticist at Trent University in Ontario, has confirmed, through genetic testing, that all 2000 or so of the surviving eastern wolves in Ontario’s Algonquin Park have some coyote DNA in their genes. In White’s view, such genetic diversity is a kind of insurance policy against major shifts in the environment that might otherwise make a species extinct.”
Twelve – Are we Polyploid?
Thirteen – the Genie that Controls the Genes
p292-3 “Our final stop on this odyssey brings us face to face with a beguiling and potentially very important force… It is called “epigenetics” and it is defined as the study of how stable changes can take place in a cell, tissue, organ or entire life form, independently of changes in its DNA sequences – in other words, it amounts to an additional non-DNA layer of control over our genes, or even over whole chromosomes. That such a system of control should exist at all is astonishing, for it suggests the power we would expect of a master controller – a genie that controls the genes.
How, for example, does this differ from what we have come to expect from genetics? A single example drives home the difference: for at least a century we have compared identical twins because they have an identical genetic make-up, but w contrast the same identical twins to show how, epigenetically, they are significantly different. Another, very important, difference is that where genes are not responsive to the environment, being fixed in their sequences unless damaged by toxic events such as irradiation, the epigenetic controllers are capable of responding to the environment: indeed, in certain aspects epigenetics may have been honed by evolution to do exactly that. This is how plants know that spring has come. As we shall discover, as we journey on into the succeeding chapter, this same system of environmental influence is of major interest to medicien. It is ironic that these “acquired” epigenetic systms are capable of being inherited across generations for this was the basis of the much-derided system of evolution first proposed by the great French biologist Jean-Baptiste Lamarck.”
p299-302 “On Day 1 of your origins, your conception as opposed to your birth day, first cleavage of that fertilised cell, or “zygote”, took place. You were now tow coned cells, each inheriting matching pairs of 22 chromosomes from your parents in addition to the two sex-determining chromosomes. If, in addition to the single X chromosome from your mother, you inherited an X chromosome from your father, you were now female: if a Y chromosome, you were now male. At his very early stage in your developmental journey, the normal silencing of genes through the epigenetic mechanism of methylation (we shall come to it shortly) was switched off. .What this might mean, in terms of the vast presence of endogenous retroviruses, is unknown…
“By Day 4, you became a solid ball of 16-32 cells,which, by the following day, turned into a hollow embryo known as a “blastula”, with an outer wall of cells and an inner cell mass surrounding the fluid-filled core. You subsequently grew out of that inner cell mass, known as the “embryological disc”. Over the following couple of days, and with the invaluable help of your symbiotic human endogenous retroviruses, you attached yourself to the lining of your mother’s womb, where you burrowed in and implanted, making yourself a snug and well nurtured home for the duration of this stage of your existence. You decided it was time to let mother know you were there, so you began to secrete the hormone human chorionic gonadotrophin, or HCG, which entered your mother’s circulation and stimulated her ovaries to produce oestrogen and progesterone – you did not want her to shed the lining ofthe womb, through the now unwanted mechanism of menstruation, not now that you were nestling in it.
“Over days 7 to 10, an indentation pushed into your blastula wall, signalling the start of your internal cavities. Up to this point, each of your cells was still a clone of that first fertilised cell. But with gastrulation, those critical EvoDevo signalling chemicals determined the genetic cascades that would make you undergo the first great developmental change that would differentiate your cells into the three fundamental types that would fashion all your adult tissues and organs: the “ectoderm” that would become your skin and nervous system, the “endoderm” that would form the lining of your gut and your internal organs, and the “mesoderm” that would become your muscles, bones and heart. I’m afraid that that first indentation would not become your mouth, but rather the opening at the latter end of your intestinal tract, your anus. We humans, like all vertebrates, begin our developmental journey anus first, and with it our bilateral symmetry is set, as opposed to, say, a starfish, who’s development is radially symmetrical. Your future mouth would have to bite its way through to the surface at the other end. by days 15-21, your developmental inheritance, and in particular your HOX genes – quadruplicated as a result of your 2R genomic inheritance – kicked in.
“From now on the side-shoots from the established central axis are getting their HOX-directed instructions, with the front end taking on the first indications of a head and the rear end taking the rudimentary form of a tail, with two parallel rills appearing along your front-to-back axis, heralding the “neural groove” that will fold over into a cylinder to form your future spinal chord and, at the head end, the brain… By Day 21 you have vestigial gills, relics of a marine past and known to developmental biologists as “pharyngeal arches”, together with a more pronounced stubby tail. These pharyngeal arches, if they persist beyond embryology, may give rise to cysts and other abnormalities that may require surgery. As early as 12 weeks most of your organs and body parts are pretty much developed, with the exception of your brain and lungs. From now on all that most of your organs need to do is to grow – but even at birth your brain, so large and so complex in proportion to your body size, arrives into the world lacking much of its essential development. during the early days after birth, your brain adds approximately a quarter of a million nerve cells every minute to its mass, and this colossal increase in size and complexity continues for the first two years after your birth.
“Thus, in you as an individual, embryological, and post-embryological, development is an exceedingly complex, pre-programmed and minutely planned process – a process that can sometimes go awry. Perhaps we should not be surprised that, depending on definitions, problems arise in anything from 2..4% to 5% of individuals. We have also seen during the broader odyssey of this book, that those very same driving mechanisms that control our evolution, and the intricate processes that govern our embryology, are the same mechanisms that give rise to the genetic basis of disease, whether it manifests at birth or in later life.”
Fourteen – the Coming Ephiphany
p319 “The blue-headed wrasse inhabits the coral reefs of the Caribbean. The male, dominant and pugnacious sports a dashingly Technicolor coat of blue, white and green, separated by thick black stripes, while the physically smaller females that make up his harem affect a more reticent composure, and cloak themselves in subdued yellow, with silver underbelly but if the male dies, or otherwise absconds from the scene, the largest of the females changes sex, her ovaries shrink and new testes sprout, all within a day or two, and she flaunts her new coat of dashing blue, white and green, and affects a macho behaviour to suit, so that, gender reassignment complete, she becomes, in flesh and in spirit, the new dominant patriarch.”
It makes one wonder if lewis Thomas was not exaggerating in his observations:
As a species, taking all in all, we are still too young, too juvenile, to be trusted. We have spread across the face of the Earth in just a few thousand years, no time at all as evolution clocks time. Covering all liveable parts of the planet, endangering other forms of life, and now threatening ourselves … what our species needs most of all, right now, is a future.
“How relevant then is this novel and expanding discipline of epigenetics, which is integral to the biological disciplines while a the same time linking them, in so many intimate and subtle ways, to the environment!”
Incidentally, I found this: UCSC Human Genome Browser
186 Days to Dec 21st 2012