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> Possible dormant virus inside all of us?, We might all be... shredded apart by microscopic 'creatures'?
lokum
post Aug 10, 2008, 06:48 PM
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I had a really disturbing idea recently about viruses:

Viruses reproduce through either the lytic cycle or the lysogenic cycle. When they use the lysogenic cycle, their DNA becomes part of the host cell's chromosome, right? So once the cell undergoes mitosis and divides, the viral DNA gets copied into the two new daughter cells. This goes on for a while, increasing exponentially, until something activates the virus. Once activated, the virus hijacks the cell and has it make viral parts, assemble them, and then the newly made viruses break out (and destroy) the cell they were once in.

If this occurs in mitosis, why not meiosis as well? Say, that, one day, a virus is embedded into a cell located in the gonads which is undergoing meiosis. Let us say that this is the sperm cell. Over yonder somewhere, the same is happening in an egg cell. After some time, the two people with these cells meet and decide to have a child. When the child is conceived, it just so happens that the sperm that fertilizes the egg contains the viral DNA (likewise, the egg contains the same viral strand). Now we have a zygote with a virus in it which is about to undergo its first cell division to make trillions of stem cells which all eventually make up a whole human being... What would happen once the virus is triggered? Would every cell in the child's body begin to be ripped apart?

It sure is a frightening thought, and would make a great sci fi movie, but is it possible? Could it mean that possibly, by some slight chance, we all just might have a virus waiting to be triggered inside us?

The only argument I have been able to come up with against this is that the virus would know that doing this would cause many potential hosts to be killed, and it would eventually run out of hosts if it wasn't able to use hosts from different species. But how could a virus 'know'? Most scientists are not ever sure if viruses are alive. Do they even metabolize energy?

Ahhh, I hope I am wrong.
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Phi
post Aug 10, 2008, 11:33 PM
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Looking on a grand scale, we could be a bacteria or a virus...luckily we have a choice to be neither
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Rick
post Aug 11, 2008, 08:00 AM
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There's already a science fiction book on this idea: Darwin's Radio, 1998, by Greg Bear.
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trojan_libido
post Aug 12, 2008, 01:08 AM
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Interesting thoughts. I read that our existence is reliant on the fact we can (or have been able to in the past) integrate a virus' DNA into our own. There is evidence that our DNA evolved to include a virus which is triggered whenever a woman falls pregnant. The virus enables the 'alien' entity to grow in the womans body without being rejected. So if it wasn't for this virus integration, we wouldn't be here!
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Rick
post Aug 12, 2008, 07:25 AM
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Pregnancy and reproduction are common to a large group of animals and plants, so that viral innovation must happened billions of years ago.
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lokum
post Aug 12, 2008, 06:37 PM
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I guess that answers my question then. I never thought of a fetus as an alien creature, though. The theory that human reproduction is dependent on a virus which is triggered when a women is impregnated is really interesting.

I hope that there are no modern, harmful viruses which can survive (although I see no reason why not) meiosis. Even then, they wouldn't have to worry about surviving, just passing their integrated DNA on...


Out of curiosity, trojan_libido, would happen to remember where you read that? I'd like to read more about this because its been stuck in my head for some time now. Also, thank you Rick for the title of the book. I've read a few books by Bear and I enjoy his writing.
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trojan_libido
post Aug 13, 2008, 05:02 AM
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I only know its in a series of science books spliced with a story of satirical humour based in Discworld. Basically some wizards create 'Roundworld' in a protective field, and begin to argue about its differences to their world and the development of it. These parts are only a few pages between the meat and bones of it which is about strange scientific concepts and misconceptions - or 'lies to children' as TPratchett likes to say.

Dont be put off by the title, the fiction is just a vehicle for the science!

http://www.amazon.com/Science-Discworld-Te...t/dp/0091886570
http://www.amazon.com/Science-Discworld-II.../ref=pd_sim_b_1
http://www.amazon.com/Science-Discworld-II.../ref=pd_sim_b_2

If you don't fancy these excellent books, let me know and I'll try and dig through them and find some scientific terms to help you search for more info.
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Phi
post Aug 13, 2008, 05:04 AM
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Evolution and God can be the same??? Holy Shi T
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trojan_libido
post Aug 13, 2008, 11:53 PM
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Lol Phi, did I miss a post or something?
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Phi
post Aug 14, 2008, 03:51 AM
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Did you still follow?
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lokum
post Aug 14, 2008, 07:10 AM
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QUOTE(Phi @ Aug 13, 2008, 05:04 AM) *

Evolution and God can be the same??? Holy Shi T


What do you mean?
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Phi
post Aug 14, 2008, 02:06 PM
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I heard this theory a while ago incorporating the bible: God could have just made bacteria and everything eventually evolved from that
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Joesus
post Aug 14, 2008, 04:30 PM
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If you liked that theory you might like the Urantia book...
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trojan_libido
post Aug 14, 2008, 11:29 PM
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If anything Phi, God included everything and 'all' God did was explode for some unknown reason and set everything into motion with the resonance from this explosion. (Explode is not the reality of course, but it suits). This motion (the path of God), eventually gained enough complexity to create what we class as living organisms, which gained momentum until you get higher primates.

I have trouble thinking that the original moment of creation (spiritual or Big Bang) happened without a cause or reason. Life is teeming out of every possible nook and crevice, often with us having to forcefully kill it (weeds and insect pests), so I tend to believe the miracle of Creation is not an accident of circumstance but a trend towards higher and higher evolution.

Many people here and elsewhere reject the idea that technology is also an evolution, but what else can the creation of the created be? Its clearly a massive leap forward for evolution when its no longer bound by the slow laws of chemistry and extremely slow development of biology.

Hypothetical statement alert!
What if bacterium became sentient enough to form lasting bonds and partnerships and form a society? If it evolved up to work together in various ways and eventually the different aspects of the society evolved into the tasks assigned by the group. What if the result after millions of years was a much larger animal like a bee or wasp - the original bacterium now totally reliant on the overall wellbeing of the wasp so the individual identity becomes lost and only the wasp as an entity is left.
</speculation off>

It amazes me how many systems and living creatures are on and within us - nested and fractal symbiosis.
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Phi
post Aug 16, 2008, 01:42 AM
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No disagreements there, and the urantia book seems interesting. What have you taken from it Joesus
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trojan_libido
post Oct 03, 2008, 10:23 AM
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QUOTE("Science of Discworld 3 - Darwins Watch)
One of the things that really worried Darwin was the existence of parasitic wasps - a fact that has influenced our Discworld tale, but has gone unremarked until now in the scientific commentaries. Parasitic wasps lay their eggs in other insects' larvae, so that as the wasp eggs grow into wasp larvae, they eat their hosts. Darwin could see how this might have happened on evolutionary grounds, but it seemed to him to be rather immoral. He was aware that wasps don't have a sense of morality, but he saw it as some kind of flaw on the part of the wasps' creator. If God designed each species on Earth, for a special purpose - which is what most people believed at the time - then God had deliberately designed parasitic wasps, whose purpose was to eat other species of insect, also designed by God. To be so eaten, presumably.
Darwin was fascinated by such wasps, ever since he first encountered them in Botafogo Bay, Brazil. He eventually satisfied himself - though not his successors - that God had found it necessary to permit the existence and evolution of parasitic wasps in order to get to humans. This is what the quote at the end of Chapter 10 alludes to. That particular explanation has fallen out of favour among biologists, along with all theist interpretations. Parasitic wasps exist because there is something for them to parasitise - so why not? Indeed, parasitic wasps play a major role in controlling many other insect populations: nearly one-third of all of the insect populations that humans like to label `pests' are kept at bay in this manner. Maybe they were created in order for humans to be possible ... At any rate, the wasps that so puzzled Darwin still have much to tell us, and the latest discovery about them threatens to overturn several cherished beliefs.

Strictly, the discovery is not so much about the wasps, as about some viruses that infect them ... or are symbiotic with them. They are called polydnaviruses.

When mother wasp injects her eggs into some unsuspecting larva, such as a caterpillar, she also injects a solid dose of viruses, among them said polydnaviruses. The caterpillar not only gets a parasite, it gets an infection. The virus's genes produce proteins that interfere with the caterpillar's own immune system, stopping it reacting to the parasite and, perhaps, rejecting it. So the wasp larvae munch merrily away on the caterpillar, and in the fullness of time they develop into adult wasps.
Now, any self-respecting adult parasitic wasp obviously needs its own complement of polydnaviruses. Where does it get them? From the caterpillar that it fed on. And it gets them (just as mother did) not as a separate infective `organism', but as what is called a provirus: a DNA sequence that has been integrated into the wasp's own genome.
Many genomes, probably most if not all, include various bits of viruses in this way. Our own certainly does. Transport of DNA by viruses seems to have been an important feature of evolution.

In 2004 a team headed by Eric Espagne worked out the DNA sequence of a polydnavirus - as one does - and what they found was dramatically different from what anyone had expected. Typical virus genomes are very different from those of 'eukaryotes'- organisms whose cells have a nucleus, which includes most multi-cellular creatures and many single-celled ones, but not bacteria. The DNA sequences of most eukaryote genes consist of `exons', short sequences that collectively code for proteins, separated by other sequences called introns, which get snipped out when the code is turned into the appropriate protein. Viral genes are relatively simple, and typically they do not contain introns. They consist of connected code sequences that specify proteins.-This particular polydnavirus genome, in contrast, does contain introns, quite a lot of them. The genome is complex, and looks much more like a eukaryote genome than a virus genome. The authors conclude that polydnavirus genomes constitute `biological weapons directed by the wasps against their hosts'. So they look more like the enemy's genome than that of an ordinary virus.

Numerous examples, old and new, disprove every aspect of the folk version of evolution and DNA. We end with one that looks especially important, discovered very recently, and whose significance is just becoming seriously apparent to the biological community. It is probably the most severe shock that cell biology has received since the discovery of DNA and the wonderful `central dogma': DNA specifies messenger-RNA which specifies proteins. The discovery was not made through some big, highly publicised research programme like the human genome project. It was made by someone who wondered why his petunias had gone stripy. When all the world is chasing `the' human genome, it's not easy to get research grants to work on stripy petunias. But what the petunias revealed is probably going to be far more important for medicine than the entire human genome project.
Because proteins are the structure of living creatures, and because as enzymes they control the processes of life, it has seemed obvious that DNA controls life, that we can `map' DNA code on to all the important living functions. We could assign a function to each protein, so we could assume that the DNA that coded for that protein was ultimately or fundamentally responsible for the corresponding function. Dawkins's early books reinforced the idea of one gene, one protein, one function (although he carefully warned his readers that he didn't want to give that impression), and this encouraged such media exaggerations as calling the human genome the Book of Life. And the `selfish gene' image made it entirely credible that huge stretches of the genome were present for solely selfish reasons - that is, for no reason related to the organism concerned.

Biologists employed - as so many now are - in the biotechnology industries serving agriculture, pharmacy, medicine, even some engineering projects (we don't mean just `genetic engineering' but making better motor oils), all subscribe to the central dogma, with a few minor modifications and exceptions. All of them have been informed that nearly all of the DNA in the human genome is `junk', not coding for proteins, and that although some of it may be important for developmental processes or for controlling some of the `real' genes, they really don't need to worry about it.

Admittedly, quite a lot of junk DNA seems to be transcribed into RNA, but these are just short lengths that sit about briefly in the cell fluids and don't need to be considered when you're doing important proteinmaking things with the real genes. Recall that the DNA sequences of real genes consist of a mosaic of `exons' which code for proteins, separated by other sequences called introns. The introns have to be cut out of the RNA copies to get the `real' protein-coding sequences, called messenger-RNAs, which lace into ribosomes like tapes into a tape player. Messenger-RNAs determine what proteins get made, and they have sequences on their ends that label them for making many copies of a protein or for destruction after only a couple of protein molecules.
Nobody worried much about those snipped-out introns, just bits of RNA drifting aimlessly around in the cell till they got broken up by enzymes. Now, they do worry. Writing in the October 2004 Scientific American, John Mattick reports that

The central dogma is woefully incomplete for describing the molecular biology of eukaryotes. Proteins do play a role in the regulation of eukaryotic gene expression, yet a hidden, parallel regulatory system consisting of RNA that acts directly on DNA, RNAs and proteins is also at work. This overlooked RNA signalling network may be what allows humans, for example, to achieve structural complexity far beyond anything seen in the unicellular world.

Petunias made that clear. In 1990 Richard Jorgensen and colleagues were trying to breed new varieties of petunias, with more interesting, brighter colours. An obvious approach was to engineer into the petunia genome some extra copies of the gene that coded for an enzyme involved in the production of pigment. More enzyme, more pigment, right?
Wrong.
Less pigment?
No, not exactly. What previously was a uniformly coloured petal became stripy. In some places the pigment was being produced, elsewhere it wasn't. This effect was so surprising that plant biologists tried to find out exactly why it was happening. And what they found was `RNA interference'. Certain RNA sequences can shut down a gene, prevent it making protein. It happens in many other organisms, too. In fact, it is extremely widespread. And it suggests something extraordinarily important.

The big question in this area, asked many times and largely ignored, has always been: if introns (which occupy all but one-twentieth of a typical protein-coding gene) have no biological function, why are they there? It is easy to dismiss them as relics of some dim evolutionary past, no longer useful, lying around because natural selection can't get rid of things that are harmless. Even so, we can still wonder whether introns are present because they do have some useful function, one that we haven't yet worked out. And it's starting to look as if that may be the case.

For a start, introns are not that ancient. It now seems that they became incorporated into the human genome relatively recently. They are probably related to mobile genetic elements known as group II introns, which are a `parasitic' form of DNA that can invade host genomes and then remove themselves when the DNA is expressed as RNA. Moreover, they now seem to have a role as 'signals' in the regulation of genetic processes. An intron may be relatively short, compared to the long protein-coding sequences that arise when the introns are snipped out, but a short signal has advantages and can do quite a lot. In effect, the introns may be genetic 'txt msgs' in the mobile phone of life. Short, cheap, and very effective. An RNA-based `code', running parallel to the DNA double helix, can affect the activity of the cell very directly. An RNA sequence can act as a very specific, well-defined signal, directing RNA molecules to their targets in RNA or DNA.

The evidence for the existence of such a signalling system is reasonable, but not yet undeniable. If such a system does exist, it clearly has the potential to resolve many biological mysteries. A big puzzle about the human genome is that its 34,000 genes manage to encode over 100,000 proteins. Clearly `one gene one protein' doesn't work. A hidden RNA signalling system could make one gene produce several proteins, depending on what the accompanying RNA signal specified. Another puzzle is the complexity of eukaryotes, especially the Cambrian explosion of 525 million years ago, when the range of terrestrial body-plans suddenly diversified out of all recognition; indeed, was more diverse than it is now. Perhaps the hypothetical RNA signalling system started to take off at that time. And it's widely known that the human and chimpanzee genomes are surprisingly similar (though the degree of similarity seems not to be 98 per cent as widely quoted even a few years ago). If our RNA signals are significantly different, that would be one way to explain why humans don't greatly resemble chimps.
At any rate, it very much looks as if all that `junk' DNA in your genome is not junk at all. On the contrary, it may be a crucial part of what makes you human.

This lesson is driven home by those business associates of parasitic wasps, the symbiotic polydnaviruses, sneakily buried inside the wasps' own DNA. There is a message there about human evolution, and it's a very strange one.

Genome-sequencing may have been oversold as the answer to human diseases, but it's very good basic science. The activities of the sequencers have revealed that wasps are not the only organisms to have bits of viral DNA hanging around in their genomes. In fact, most creatures do, humans included. The human genome even contains one complete viral genome, and only one, called ERV-3 (Endogenous RetroVirus). This may seem an evolutionary oddity, a bit of `junk DNA' that really is junk ... but, actually, without it none of us would be here. It plays the absolutely crucial role of preventing rejection of the foetus by the mother. Mother's immune system `ought to' recognise the tissue of a developing baby as `foreign', and trigger actions that will get rid of it. By `ought to' here we mean that this is what the immune system normally does for tissue that is not the mother's own.

Apparently, the ERV-3 protein closely resembles another one called p15E, which is part of a widespread defence system used by viruses to stop their hosts killing them off. The p15E protein stops lymphocytes, a key type of cell in the immune system, from responding to antigens, molecules that reveal the virus's foreign nature. At some stage during mammalian evolution, this defence system was stolen from the viruses and used to stop the female placenta responding to antigens that reveal the foreign nature of the foetus's father. Perhaps on the principle of being hung for a sheep as well as for a lamb, the human genome decided to go the whole hog [1] and steal the entire retroviral genome.

When evolution carried out the theft, however, it did not just dump its booty into the human DNA sequence unchanged. It threw in a couple of introns, too, splitting ERV-3 into several separate pieces. It's complete, but not connected. No matter: enzymes can easily snip out the introns when that bit of DNA is turned into protein. But no one knows why the introns are there. They might be an accidental intrusion. Or - pursuing the RNA interference idea - they might be much more significant. Those introns might be an important part of the genetic regulatory system, `text messages' that let the placenta use ERV-3 without running the risk of setting the corresponding virus loose.

At any rate, whatever the introns are for, warm-bloodedness is not the only trick that mammalian evolution managed to find and exploit.
Hopefully that'll answer your questions and others Lokum!
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lokum
post Oct 04, 2008, 10:49 AM
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Thank you very, very much.

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