{"id":6687,"date":"2013-10-15T12:27:24","date_gmt":"2013-10-15T16:27:24","guid":{"rendered":"http:\/\/ianchadwick.com\/blog\/?p=6687"},"modified":"2013-10-15T12:27:24","modified_gmt":"2013-10-15T16:27:24","slug":"we-are-stardust-and-viral-genes","status":"publish","type":"post","link":"https:\/\/ianchadwick.com\/blog\/we-are-stardust-and-viral-genes\/","title":{"rendered":"We are Stardust… and Viral Genes"},"content":{"rendered":"
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\"Supernova\"In her classic song, Woodstock<\/a>, Joni Mitchell ended with the chorus:<\/strong><\/p>\n

We are stardust
\nBillion-year-old carbon
\nWe are golden
\nCaught in the devil’s bargain
\nAnd we’ve got to get ourselves
\nBack to the garden<\/p><\/blockquote>\n

Which most people assume is merely poetic licence. Well, Joni wasn’t wrong: we – and every living thing on our planet – are<\/em> made of stardust. As we learn at Physics Central<\/a>:<\/p>\n

If we know how many hydrogen atoms are in our body, then we can say that the rest is stardust. Our body is composed of roughly 7×1027 atoms. That is a lot of atoms! Try writing that number out on a piece of paper: 7 with 27 zeros behind it. We say roughly because if you pluck a hair or pick your nose there might be slightly less. Now it turns out that of those billion billion billion atoms, 4.2×1027 of them are hydrogen. Remember that hydrogen is bigbang dust and not stardust. This leaves 2.8×1027 atoms of stardust. Thus the amount of stardust atoms in our body is 40%.<\/p>\n

Since stardust atoms are the heavier elements, the percentage of star mass in our body is much more impressive. Most of the hydrogen in our body floats around in the form of water. The human body is about 60% water and hydrogen only accounts for 11% of that water mass. Even though water consists of two hydrogen atoms for every oxygen, hydrogen has much less mass. We can conclude that 93% of the mass in our body is stardust. Just think, long ago someone may have wished upon a star that you are made of.<\/p><\/blockquote>\n

Mitchell’s theme was picked up by the late cosmologist, Carl Sagan, in his hit TV show, Cosmo<\/em>s. Live Science<\/a> tells us:<\/p>\n

In the early 1980s, astronomer Carl Sagan hosted and narrated a 13-part television series called “Cosmos” that aired on PBS. On the show, Sagan thoroughly explained many science-related topics, including Earth’s history, evolution, the origin of life and the solar system.<\/p>\n

Since stardust atoms are the heavier elements, the percentage of star mass in our body is much more impressive. Most of the hydrogen in our body floats around in the form of water. The human body is about 60% water and hydrogen only accounts for 11% of that water mass. Even though water consists of two hydrogen atoms for every oxygen, hydrogen has much less mass. We can conclude that 93% of the mass in our body is stardust. Just think, long ago someone may have wished upon a star that you are made of.<\/p>\n

“We are a way for the universe to know itself. Some part of our being knows this is where we came from. We long to return. And we can, because the cosmos is also within us. We’re made of star stuff,” Sagan famously stated in one episode.<\/p>\n

His statement sums up the fact that the carbon, nitrogen and oxygen atoms in our bodies, as well as atoms of all other heavy elements, were created in previous generations of stars over 4.5 billion years ago. Because humans and every other animal as well as most of the matter on Earth contain these elements, we are literally made of star stuff, said Chris Impey, professor of astronomy at the University of Arizona.<\/p>\n

“All organic matter containing carbon was produced originally in stars,” Impey told Life’s Little Mysteries. “The universe was originally hydrogen and helium, the carbon was made subsequently, over billions of years.”<\/p><\/blockquote>\n

So how did all this stardust get into out bodies? Supernovae, spewing heavy material into the vastness of space, scattering atoms and molecules at near lightspeed. Our “Garden of Eden” was the nuclear furnace of an exploding star.<\/p>\n

We are made of the material created 13-plus billion years ago, We are, as Mitchell sang, stardust<\/a>. Recycled and reused, but the stuff of the cosmos nonetheless. *<\/span><\/p>\n

And we’re also built of viral genes, a product of the evolution of life, of the co-evolution of life and that strange creature, the virus. Viruses have helped shape us, and our adaptations to the environment. That’s the premise of Frank Ryan’s latest book, Virolution<\/a>.**<\/span><\/p>\n

<\/p>\n

Viruses are odd things.<\/strong>\u00a0Somewhat scary, but very fascinating. Not life as we think of it. They are so simple as to defy most conceptions we have of how living creatures function. And so small that they make even single celled organisms look like the Death Star in comparison.<\/p>\n

Viruses are older than other forms of life, and have co-evolved with life<\/a> ever since life formed on this planet.<\/p>\n

Viruses of nearly all the major classes of organisms – animals, plants, fungi and bacteria \/ archaea – probably evolved with their hosts in the seas, given that most of the evolution of life on this planet has occurred there. \u00a0 This means that viruses also probably emerged from the waters with their different hosts, during the successive waves of colonisation of the terrestrial environment.<\/p><\/blockquote>\n

Many debates crop up in scientific literature about whether viruses are alive<\/a>. That invokes a whole discussion on how we define life. If it is defined simply as<\/a>, “the ability to move a genetic blueprint into future generations, thereby regenerating your likeness,” then viruses are alive.<\/p>\n

This Carelton University site<\/a> gives us some truly remarkable facts about viruses:<\/p>\n

It is a surprise to most who think of viruses simply as parasites that they make up the largest component of biomass on this planet (Bamford 2003, Research in Microbiology 154; 231-236). So far every living organism that has been studied to date has had at least one virus associated with it, and viruses out number all other life forms by at least an order of magnitude (Ackerman 2003, Research in Microbiology 154; 245-251). When considering that not only is viral presence on this planet all encompassing, but every sequenced organism to date has a major component of its genome that is viral in origin, it becomes apparent that viruses are integral players in the evolution of what we presently consider life.<\/p><\/blockquote>\n

One site tells<\/a> us:<\/p>\n

Viruses straddle the definition of life. They lie somewhere between supra molecular complexes and very simple biological entities. Viruses contain some of the structures and exhibit some of the activities that are common to organic life, but they are missing many of the others. In general, viruses are entirely composed of a single strand of genetic information encased within a protein capsule. Viruses lack most of the internal structure and machinery which characterize ‘life’, including the biosynthetic machinery that is necessary for reproduction. In order for a virus to replicate it must infect a suitable host cell.<\/p>\n

Viruses exist in two distinct states. When not in contact with a host cell, the virus remains entirely dormant. During this time there are no internal biological activities occurring within the virus, and in essence the virus is no more than a static organic particle. In this simple, clearly non-living state viruses are referred to as ‘virions’. Virions can remain in this dormant state for extended periods of time, waiting patiently to come into contact with the appropriate host. When the virion comes into contact with the appropriate host, it becomes active and is then referred to as a virus. It now displays properties typified by living organisms, such as reacting to its environment and directing its efforts toward self-replication.<\/p><\/blockquote>\n

\"Giant<\/a>The recent discoveries of the giant Marseillevirus,\u00a0Mimivirus and of Pandoravirus<\/a> complicate definitions, challenge assumptions<\/a>, but also open new areas for understanding the viral role in life, and in creating biodiversity:<\/p>\n

This groundbreaking research included an analysis of the Pandoravirus salinus proteome, which proved that the proteins making it up are consistent with those predicted by the virus’ genome sequence. Pandoraviruses thus use the universal genetic code shared by all living organisms on the planet.
\nThis shows just how much more there is to learn regarding microscopic biodiversity as soon as new environments are considered. The simultaneous discovery of two specimens of this new virus family in sediments located 15,000 km apart indicates that Pandoraviruses, which were completely unknown until now, are very likely not rare.
\nIt definitively bridges the gap between viruses and cells — a gap that was proclaimed as dogma at the very outset of modern virology back in the 1950s.
\nIt also suggests that cell life could have emerged with a far greater variety of pre-cellular forms than those conventionally considered, as the new giant virus has almost no equivalent among the three recognized domains of cellular life, namely eukaryota (or eukaryotes), eubacteria, and archaea.<\/p><\/blockquote>\n

Giant viruses may actually be de-evolution in action: devolved from cells<\/a> to component parts:<\/p>\n

…descendants of an ancient, free-living eukaryotic cell. Various genes and structures from that organism have gradually been lost over its long history as a parasite, leaving something that propagates like a virus, but belongs to a distinct lineage from all other viruses that we’re aware of.<\/p><\/blockquote>\n

The complex relationship among viruses, and between viruses and life, is only now being fully explored, thanks to the advancement of genetic studies and the technology to parse genetic material. Science Daily<\/a> reported in May,<\/p>\n

Radically different viruses share genes and are likely to share ancestry, according to research published in BioMed Central’s open access journal Virology Journal this week. The comprehensive phylogenomic analysis compares giant viruses that infect amoeba with tiny viruses known as virophages and to several groups of transposable elements. The complex network of evolutionary relationships the authors describe suggests that viruses evolved from non-viral mobile genetic elements and vice versa, on more than one occasion.<\/p>\n

The recent discovery of virophages inside the giant viruses, which in turn infect amoeba, has led to speculation about their origin and their relationship to other viruses and small transposable genetic elements.<\/p><\/blockquote>\n

Back to Frank Ryan and his compelling story. In a review of the book Virolution in the Wall Street Journal<\/a>, Carl Zimmer summed it up:<\/p>\n

We are part virus. This bizarre yet inescapable fact has been revealed over the past 30 years, as scientists have spelunked their way through the human genome and encountered stretches of DNA with the telltale chemical signatures of viruses. All told, they’ve found 100,000 such segments so far. As Frank Ryan explains in “Virolution,” these pieces of virus DNA ended up in our genome through a peculiar kind of infection. From time to time, viruses slipped their DNA into the eggs and sperm of our ancestors. Parents then passed down the virus DNA to their offspring. These viruses could no longer escape their hosts, but they could still make new copies of their DNA, which were then inserted back into our ancestors’ genomes. And so it is that, after millions of years of infection, viruses now make up at least 8% of the human genome. Our “own” genes\u2014the genes that encode the proteins that constitute our bodies\u2014make up a measly 1.2%.<\/p><\/blockquote>\n

In another published review<\/a>, in the magazine Symbiosis, reviewers\u00a0Ricardo Santos and Francisco Carrapi\u00e7o write,<\/p>\n

Chapter five, The Paradox of the Human Genome, starts with a reference to the DNA breakdown of the human genome, in particular the evidence that the part we normally associate with what makes us human amounts to a mere 1,5% of the whole, while the human endogenous retroviruses, or HERVs, amount to an amazing 9%. The author referred to the case of the newly discovered epidemic virus that was affecting Australian koalas as a good example of an endogenisation process of a virus that has affected the koala population during the last hundred years and which was probably introduced by a rodent. Invoking once again the concept of \u201caggressive symbiosis\u201d, the author intends to show that this concept implies various steps, ranging from the interaction between exogenous virus and host, to plague culling and partnership at the most powerful symbiogenetic level, followed by complete genomic fusion. Finally, the chapter culminates in an extended and interested conversation with the virologist Luis Villarreal, who believes that viruses, and their closely related products, make up at least 43% of the known human genome.<\/p>\n

In chapter six, entitled How Viruses Helped Make Us Human, the author frames his concept of \u201caggressive symbiosis\u201d in Darwinian and symbiotic perspective. He does so because, according to him, we cannot possibly interpret the massive viral presence in the human genome if we fail to consider both perspectives.<\/p><\/blockquote>\n

The notion that we may have viral genes in our genome isn’t really all that odd. As Ryan points out in his introduction, when the human genome was sequenced, it was discovered we had a lot in common, genetically, with other creatures:<\/p>\n

Most revealing of all was the confirmation of our common inheritance with other forms of life on Earth. For example,we share 2,758 of our genes with the fruit fly, 2,031 with the nematode worm \u2013 indeed, all three of us, human, fly, and worm, have 1,523 genes in common.<\/p><\/blockquote>\n

\"Pandoravirus\"<\/a>Ryan’s argument in his book is that, “this shared inheritance could not have arisen by chance.” But if you’re hunting for some hook to hang an ID hat on, you’ll be disappointed. no deus ex machina pulling the strings here.<\/p>\n

The mechanism is viruses and what changes they bring to our genetic makeup.<\/p>\n

Not really news if you’ve been following some of these developments (see this piece on<\/a>\u00a0the transport of the “Influenza Virus Genome from Nucleus to Nucleus,” for example), but a story well told and another insight into the mechanics of evolution. Ryan ties together several strands of the tale so readers don’t need to scour the internet looking for connections. But he also pushes forward some bold ideas.<\/p>\n

Ryan himself points out historical precedent, in chapter eight<\/a> on auto-immune diseases:<\/p>\n

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 \u2018The source of self: genetic parasites and the origin of adaptive immunity\u2018 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 \u201cself\u201d, through complex evolutionary interactions between phage viruses and their host bacteria.<\/p><\/blockquote>\n

Equally intriguing as the evolutionary implications are the implications for medicine (and how these viral hitchhikers affect our health or cause disease). It starts to get complicated here. Blogger Sheila Newman<\/a> explains it thus:<\/p>\n

…different animal populations carry different viruses as part of their genome, and sub-populations of species may carry viruses that are dangerous to other members of the same species. Ryan discusses this prospect in a study of different populations of koala in Australia, for instance.<\/p>\n

Ryan goes on to write about how it is likely that certain diseases, including diabetes mellitus and multiple sclerosis, result when this mutually beneficial relationship breaks down in humans for reasons that need more exploration. This is also an explanation for cancer and the increase in cancers in elderly people whose systems, as they become more disorderly, are unable to maintain an effective immune system.<\/p>\n

Back to how the endemic viral material of different populations and species can be dangerous for that of other populations and species: The fact that viruses embodied in animal cells are dangerous to other populations which are not immune to those viruses, means that where one population \u2013 of the same species but from a different area – encroaches on another population\u2019s territory, the encroaching population runs the risk of succumbing to viruses carried by the first. Other species can also be affected.<\/p><\/blockquote>\n

Just how astounding this whole process is, Ryan tells us in the opening for Chapter 13<\/a>, titled ”\u00a0The Genie that Controls the Genes:”<\/p>\n

Our final stop on this odyssey brings us face to face with a beguiling and potentially very important force\u2026 It is called \u201cepigenetics\u201d 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 \u2013 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 \u2013 a genie that controls the genes.<\/p>\n

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.<\/p>\n

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 medicine. It is ironic that these \u201cacquired\u201d epigenetic systems 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.<\/p><\/blockquote>\n

Snips, and snails and puppy dog tails no more. Today we’re stardust and viral genes, an of mix or macro and micro. Being human has never been so interesting. And for readers, Frank Ryan’s new book makes it more understandable.<\/p>\n

~~~~~<\/strong><\/p>\n

*<\/span>\u00a0Astrobiologist\u00a0Richard Boyd<\/a>\u00a0has suggested that, even further than stardust, our very amino acids are cosmic relics:<\/p>\n

Where were the amino acids, the molecules of life, created: perhaps in a lightning storm in the early Earth, or perhaps elsewhere in the cosmos? This book argues that at least some of them must have been produced in the cosmos, and that the fact that the Earthly amino acids have a specific handedness provides an important clue for that explanation. The book discusses several models that purport to explain the handedness, ultimately proposing a new explanation that involves cosmic processing of the amino acids produced in space.<\/p><\/blockquote>\n

**<\/span> Ryan is working on another book – Metamorphosis<\/a> – which might be considered a companion or even sequel to Virolution.<\/p>\n","protected":false},"excerpt":{"rendered":"

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In her classic song, Woodstock, Joni Mitchell ended with the chorus: We are stardust Billion-year-old carbon We are golden Caught in the devil’s bargain And we’ve got to get ourselves Back to the garden Which most people assume is merely poetic licence. Well, Joni wasn’t wrong: we – and every living thing on our planet – are made of stardust. As we learn at Physics Central: If we know how many hydrogen atoms are in our body, then we can say that the rest is stardust. Our body is composed of roughly 7×1027 atoms. That is a lot of atoms! \u2026…… click below for more \u2193<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_hide_featured_image":false,"_jetpack_featured_image_duplicate_dismissed":0,"_jetpack_feature_clip_id":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[8,261,5,72],"tags":[367,166,93,366,147,29],"class_list":["post-6687","post","type-post","status-publish","format-standard","hentry","category-books","category-critical-thinking-2","category-science-technology","category-books-by-the-bedside","tag-book-review","tag-critical-thinking","tag-evolution","tag-genetics","tag-reading","tag-science"],"a3_pvc":{"activated":true,"total_views":10357,"today_views":0},"jetpack_publicize_connections":[],"jetpack_sharing_enabled":true,"jetpack_likes_enabled":true,"jetpack-related-posts":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/posts\/6687","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/comments?post=6687"}],"version-history":[{"count":9,"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/posts\/6687\/revisions"}],"predecessor-version":[{"id":6702,"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/posts\/6687\/revisions\/6702"}],"wp:attachment":[{"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/media?parent=6687"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/categories?post=6687"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ianchadwick.com\/blog\/wp-json\/wp\/v2\/tags?post=6687"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}