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 Post subject: Random question for science gurus...viruses
PostPosted: Wed Feb 06, 2008 12:15 am 
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Ok, I am admittedly a linguist, bibliophile and in love with all that is words...so I have to admit that science has to be really clearly explained to me for me to get something. (I'm not one who can just be told "that's the way it is" and go on...)

Anyhow, in college I had an extremely frustrating experience with my bio prof when I asked about viruses and how they are not considered to be "alive".

Anyone care to venture on explaining this phenomenon to me in a clear way that I will be able to understand. (And no, I'm not retarded, I just need more info than "just believe it" crap)

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PostPosted: Wed Feb 06, 2008 8:11 pm 
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I used to say they were alive, the I heard about prions (more on them later).

Viruses are simply parasitic complex molecules. All living things need energy. A virus will never be seen feeding, or metabolizing anything. When it encounters its host, it injects its genetic material which causes the cell to produce more viruses. They dont eat or consume the cells, they just use our process of gene duplication for their own benefit.

Now, bacteria, on the other hand, consume our cells and/or use them for some sort of nutrition.

Viruses also dont have cells. A cell is considered the simplest for of life, and a virus is the equivalent of a coating over DNA or RNA. (although I think many prokaryotes are like this as well)

There are also some baddies out there called prions. Prions are proteins gone bad. (Mad Cow disease, Chronic Wasting Disease). Many of our protiens do what they do because of their physical shape. Our body works a lot like a puzzle. The pieces all have a special shape and fit in a specific place. Well, prions have a really jumbled up shape and can no longer fit where they are supposed to.

But our troubles dont stop there....

When a prion makes contact with a healthy protein, it converts it into a prion as well. Sort of like getting bit by a zombie. Now a few bad eggs wont do a whole lot to you, but their damage increases exponentially. Worst part is, there really is no cure for anyone/anything infected with these. Not only are out bodies not able to kill prions, but its almost impossible to sterilize anything that has been in contact with them. Heat, chemicals and radiation all have little, if any effect on them. About the only way to get rid of them is to use an auto-clave. This uses pressure to heat water way above its boiling point in order to kill these buggers.


So, its clear that a prion isnt life. Its just a protein. And a virus is actually more simple than that, its simply a code with a shell. So its not a stretch to see why a virus isnt, and shouldnt be classified as a life.

A common problem that science has with the public is definitions. Many non-science people like to substitute knowing definitions for knowledge. I actually has a class (animal behavior) where 3/4 of our time was spent trying to define words. And most of these were seemingly easy words such as information, signal, communication, etc... Defining words and concepts is NOT as easy as looking in the dictionary. In order to understand and scientific concept definition, you must first be able to understand all the baggage associated with that concept. I really wish global warming was as simple as "a globe thats warming" and that the carbon cycle was as easy as live, die, decompose, eat..... but its not. And because its not, it becomes almost impossible to define.

This is why I hope that my examples above go somewhat above a simple definition and how something does/doesnt fit and instead helps to explain more on the concept of life, and its components.

I hope this help, if you need any more clarification, let me know.

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PostPosted: Thu Feb 07, 2008 1:14 am 
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Yea....what he said.

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PostPosted: Thu Feb 07, 2008 7:00 am 
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Wonderful post, nygg!

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PostPosted: Thu Feb 07, 2008 9:47 am 
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On my way to work, so I will have to put more later...

anyhow, thanks for the answer. Of course, I still have questions.

I don't understand how something non-living can, on its own, complete any task. Like a pen on my desk doesn't do anything, because its not alive, it cannot replicate itself, eat...all that shit. The only way it "does' anything is if I pick it up and write with it, or stab someone with it, whatever I chose to do...

Viruses, on the other hand, appear to have functions entirely on their own without me picking it up and stabbing someone with it.

How can it have function, without being somewhat "alive"...?

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PostPosted: Thu Feb 07, 2008 3:03 pm 
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Yeah, and not requiring food only a host, makes it somewhat parasitic, but that would prove intent and only thinking creatures have intent. Could it be like a brain cell that doesn't require food or oxygen to be sought after, just provided by a host for its existance so it can perform its intended purpose.

I have also heard they can survive in many places where we would die, and that viruses could be the actual seed of life transmitted through flangellate looking comets seeding the planets where other forms of life awakens it.

Perhaps their real function is unknown because we can't understand it having a function and time has covered its original purpose. It is after all a very simple form of life, isn't it? Or is it more progressed than we can comprehend? Does it have a function to be part of existence beyond just infecting us? Or is it by infection that mutations started and thus the virus could be another missing link in the development of life?

So many questions and only GG to depend on. :| :shock: :D

I'm sure he'll help us dispel the myths and give us the best answer he can. I like the way they adapt to fit any problem, like there is no impossibilities in life. Seems they may be the magic bullet for good or harm, but either way it proves that survival is stronger than life itself, as they can be dead until required to live. Fascinating creatures, if creatures they are.

Like life imitating life, its truth being held back from us and we can only guess at the best explanation once again. Lifes mysteries- will we ever get it right on? The fun seems to be in the quest and not the finding out, which ends our guessing. Guessing seems to keep us progressing and finding out stifles the search to know assumptions. Seems not knowing has given us a purpose and helps define our meaning.

And that might explain our draw to religion and science.

Imagine, viruses as the first ET's, heaven sent! :? 8)

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PostPosted: Fri Feb 08, 2008 11:48 pm 
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lefty wrote:

I don't understand how something non-living can, on its own, complete any task.
hmm..complete a task? You computer completes tasks on its own. And if you wanna say its programming doesnt count, remember viruses also have programming.

Heck, some computers can be programmed to build other computers! Thats just like reproduction! Its all in the programming.


[/quote]How can it have function, without being somewhat "alive"...?[/quote] Alive? Perhaps "alive" isnt the best definition because many non-living things can appear "alive".

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PostPosted: Fri Feb 08, 2008 11:59 pm 
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DO.g's wrote:

Perhaps their real function is unknown because we can't understand it having a function and time has covered its original purpose. It is after all a very simple form of life, isn't it? Or is it more progressed than we can comprehend? Does it have a function to be part of existence beyond just infecting us?
Infecting things just happens to be what works. Nature doesnt make any choice in what it does, it just works with whats available. Even with the canine, with the sharp teeth isnt supposed to eat meat, it just happens to be that thats what works best for the canine. Im really struggling with the proper words right now, so ill leave this though here until i come up with something better. (ive been up since 6 am and its now 10pm. im pooped!)

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Or is it by infection that mutations started and thus the virus could be another missing link in the development of life?
The simplest must come first. RNA came first, and there had to be mutations before there could be a virus.

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So many questions and only GG to depend on. :| :shock: :D
Crap, I dont know if I can handle the responsibility! :)

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I like the way they adapt to fit any problem, like there is no impossibilities in life. Seems they may be the magic bullet for good or harm, but either way it proves that survival is stronger than life itself, as they can be dead until required to live. Fascinating creatures, if creatures they are.
Well, life in general is fascinating. Bacteria that live in INSANE temperatures and pressures. Life has adapted to be able to survive in every nook and cranny of this big blue ball. It has become adapted to the most hostile conditions we know of. Its simply amazing.



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Imagine, viruses as the first ET's, heaven sent! :? 8)
Hey, many think so!

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PostPosted: Sat Feb 09, 2008 12:08 pm 
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Ok, but my thing is that I don't understand how it functions. If it is programmed and completes a task, yet isn't electronic or running on gears or any of that. Then how can it have a function, actually DO something when there aren't batteries?

Viruses DO things. And I realize there is a "program" but wouldn't that program be similar to what "Living" things have programmed in them? I just don't understand how something can do something on its own, with no outside initial start, and not be considered alive.

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PostPosted: Sat Feb 09, 2008 3:13 pm 
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My son called me yesterday. He said he'd been out of work for two days with a serious case of bronchitis. He said so many of the police force were out with the illness, the lieutenants and the Police Chief were having to step in and take over the duties of corporals and sergeants. I asked him how it got started, and he said the first one to get sick was the dispatcher!

After she went home for a few days, everyone else began to get sick. The doctor my son went to told him that he'd seen a parade of school-age kids with bronchitis, flu, and pneumonia.

This is in west Texas. Now, I don't think the dispatcher "infected" everybody but it does seem strange. Thoughts? :?

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PostPosted: Sat Feb 09, 2008 3:31 pm 
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I don't think it makes any conscious choices until it becomes active when it encounters the proper conditions. Until then it could be considered inanimate. It's existence depends on life to become what its programming has set it in motion to do- which seems to be in propagating itself and spreading. I guess that means there were other forms of life already around so it could do the natural thing and that life is all connected to the same roots. A DNA/RNA thing.

Sounds like it does embrace all the actions of life without the problems involved with life or death. A non-thinking non-sentient being that has features of a parasite. Seems like the ultimate unconscionable entity that lives when and where it can flourish- the ultimate trigger to stimulate growth in cells as it feeds/reproduces symbiotically. Who knows now what benefits it has performed in our shared historic pasts. If the common cold is an example, it uses the host for its purpose and then departs to find other receptive conditions to continue its spreading.

If they can survive the conditions of space, absolute zero and heat of entry, then they are closer to indestructible than anything we have encountered. Perhaps this little article will help to give a history of possibilities-

http://www.panspermia.org/comets.htm
Quote:
Christopher Chyba, Paul Thomas, Leigh Brookshaw and Carl Sagan wrote a study of this problem, published in Science in 1990, entitled "Cometary Delivery of Organic Molecules to the Early Earth" (12). They carefully calculate the heat generated by high speed impacts with Earth, and then conclude that life's building blocks (not whole cells) could arrive intact. It is reasonable to extend their conclusion to cells, by expanding the scope of their study. Chyba and his coauthors in 1990 admittedly do not examine the case of a comet exploding before impact. However most comets, indeed most large meteoroids of any type except iron ones would explode before impact. In 1992 Chyba and Sagan (13) did address the explosion of comets in the atmosphere and found that for the delivery of intact organic compounds at least, this method of transfer was far more effective than comets that collide with the surface.

The best known atmospheric explosion of a meteoroid happened eight kilometers above Tunguska in central Siberia on June 30, 1908. The explosion flattened the forest for roughly 15 kilometers in every direction. The object was most likely an asteroid, perhaps 60 meters in diameter, because a comet would have exploded higher in the atmosphere. Our knowledge of this event is indirect because no one investigated the site until twenty years after the explosion (14). A similar atmospheric explosion, again over Siberia, occurred in 1947. We know that atmospheric explosions before impact by comets and asteroids are common. An explosion in the air would be much gentler than a collision with either Earth's hard surface or the ocean. Matter on the trailing side of a comet exploding in the atmosphere would be significantly slowed by the jolt. And matter located there would also be the best protected from the heat generated during atmospheric entry prior to the explosion...........<snip>...........On the morning of September 28, 1969, a carbonaceous chondrite fell near Murchison, Victoria, Australia. The parent object disintegrated in the air and scattered fragments over an area of about five square miles. Scientists from NASA analyzed some of the fragments and determined that they contained organic molecules which "seem to have been formed before the meteorites reached the Earth" (26). The researchers took great care to assure that the organic contents were not Earthly contaminants.

Nearly ten years later, German geologist and paleontologist Hans Dietrich Pflug also examined fragments of the Murchison meteorite. Using a new and difficult technique, he isolated from the fragments and photographed some startling things. The photographed forms clearly resemble fossilized cells and virus particles. Pflug considered the arguments for and against Earthly contamination as the source for the fossils and is convinced that the fossils came from space (27). But he is officially noncommittal as to whether they are actually what they look like-cells and virus particles. "There is no convincing evidence that the forms are more than `organized elements,' possibly some kind of prebiotic structures," he now says. Today the consensus is that all such fossils are Earthly contaminants, but the case is not settled. More research is needed.

Recently, new and better methods to conduct this kind of research have been developed by NASA researchers examining the meteorite from Mars designated ALH 84001. Fortunately, similar methods are now being applied to the Murchison meteorite, and the preliminary results are startling. Pictures made available in July, 1997, show microscopic forms in Murchison that look very lifelike.
But of course more research is needed. I will be posting about the lakes under Antartica in Science or Environment and how they may reveal some long lost secrets.

Perhaps humans are just an extension of that basic instruction as well and seek ways that succeed in their spread. We have been called a bacteria before in the Matrix, but we may share the traits of a virus as well. The fact that a virus or bacteria can fit into a cell and a bacteria can feed off other cells, proves that many symbiotic and predatory things have helped to shape us.

Maybe we have more than one set of characteristics that go way back to our initial instructions and those have become our instinctive drive. Sex, death, reincarnation, heaven- prime directives of most thought about existence and its aftermath. Our instinctive drives are the most powerful because their origins and speculations are based on the unknown as well. Many things seem to be unknown and how much of life is guided by speculations is unknown.

Quote:
Hoyle and Wickramasinghe calculated that a particle the size of a typical bacterium might get briefly heated to 500 degrees C. They then cite studies in which E. coli were subjected to close to twenty seconds of flash heating of up to 700 degrees C and survived. E. coli do not normally live in a hot environment; they live in our intestines. There are archaebacteria, however, that thrive at well above the boiling point of water, and many bacteria form heat-resistant spores. It is reasonable to assume that the sporulated forms of some of these could survive flash heating even better than normal E. coli can

The only thing we truly seem to know is that there are a lot of unknowns that drive our actions and decisions. Speculative doubt based on observation and known facts leading to assumed possibilities of origin.

The more we search the more we realize that the origins of life and speculations about death and its aftermath are the unknowns that drive our every action, consciously or unconsciously. We have just evolved an intelligence to answer these unknowns to the best of our knowledge and experience. Thus information is a question of trial and error with a preponderance towards error that makes answering certain questions such a problem. How can one know what hasn't been experienced or fully understood.

Perhaps we'll never truly know everything, but the adventure seems to be in the mystery of discovery as each piece adds to the puzzle instead of solving it. This is why we can be so overwhelmed by doubt, that it drives us to seek and find answers. The pain of not knowing is too hard to bear, so we invent all kinds of solutions that help ease the pain of not knowing.

Quote:
An array of cellular equipment that could help bacteria survive sudden heating is their set of "heat-shock" proteins. According to the textbook The Molecular Biology of the Gene (31):

"In almost all kinds of cells subject to heat shock, certain proteins (about 17 in E. coli) begin to be made much faster than usual.... Remarkably, some heat-shock proteins of widely different species are closely related; in fact, there are even similarities between those of bacteria and those of eukaryotes.... [W]e have no idea what function they have in common that is essential to save cells from the rigors of a sudden temperature rise...."
The response time of heat-shock proteins is less than a minute in the eukaryotic cells that have been observed for this response. In prokaryotic cells the response would be much quicker, because transcription is simpler and translation begins immediately. The writers of the quoted text do not consider that these proteins could help cells survive the heat of atmospheric entry. But why couldn't they?


Amazing what they speculate about a symbiotically beneficial survival technique isn't it?

I seem to be engaged in that right now! :roll: :wink: :D Hope I haven't caused too much pain. I hope I haven't opened up too many speculations that you and NYGG will find absurd, but I like to go places where few humans would bravely venture. Speculative philosophy is so random that it makes perfect sense to me. It is all we have to venture into the unknown and allow that rhythm to flow.

Doubt turns out to be our most important sense of all and unfortunately may be our demise as well. Another double helix dilemma wrapped within an enigma. Can we survive our own doubts? Will we ever know everything?

Will that take our will from us when we finally attain the knowledge of a god? Perhaps god has run out of new ideas and even he has become as old and useless to himself, as he is becoming to us. The old codger charlatan has outgrown an original purpose and meaning as a virus or bacterium does, but it stills hangs around to infect us and make us aware of our humanity. What can most humans do but pray for hope and understanding.

Enquiring minds have to know! Few can survive the limbo state of speculative doubt, but it is the edge of the knife we have to walk if we truly want to know. No one can predict the future, so we have to have signs and portents to lead us. Science is hoping and praying they can provide that solution before our doubts overtake us.

Perhaps your question may be the key to answering a lot of those mysteries- how can something be classified as a living dead entity? With a mystery like that, who knows where the answers may lie and what directions it will take us.

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PostPosted: Sat Feb 09, 2008 4:20 pm 
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lefty wrote:
Ok, but my thing is that I don't understand how it functions. If it is programmed and completes a task, yet isn't electronic or running on gears or any of that. Then how can it have a function, actually DO something when there aren't batteries?
The only function it needs to do is insert its genes into its host. For movement, it can pretty much float in the air, hang out in the water, etc... It uses us to do everything for it. When it reaches the right cell, with the right protein, it attaches and injects its DNA. It then uses YOUR body to replicate itself.

Think of it like a computer virus. They are both almost identical. They have programming (like DNA) and dont need to actively move (why did you open that email!) and use other computers to replicate.


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Viruses DO things. And I realize there is a "program" but wouldn't that program be similar to what "Living" things have programmed in them? I just don't understand how something can do something on its own, with no outside initial start, and not be considered alive.
Outside initial start? Well, all life got here without an outside initial start!

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PostPosted: Sat Feb 09, 2008 6:25 pm 
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nygreenguy wrote:
Outside initial start? Well, all life got here without an outside initial start!


I have memories that some time in the late 60s or early 70s where they mixed up a batch of "primordial soup." This consisted of the chemicals thought to be floating free early in the formation of the planet. They then applied blasts of artificial lightning. What I remember is that this resulted in basic amino acids being formed, the building blocks of proteins, RNA and DNA. The scientists believed that lightening could have well served as the outside initial start.

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PostPosted: Sat Feb 09, 2008 8:31 pm 
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Wanted to get this down before it gets lost again. It 's about the RNA idea and also expands on many different theories.

http://www.panspermia.org/rnaworld.htm

There's so much good info here and one item they mention that I had never heard- the term PNA- for Peptide Nucleic Acid which is theorized to be a simpler form of NA that preceded RNA.

Quote:
Another idea is the "PNA world." Because starting the RNA world is so difficult, there probably needs to be a pre-RNA world. PNA, or peptide nucleic acid, might have some of the properties necessary to constitute that world (21). This would be pre-precellular life.


There are some common threads running through the various theories-

Quote:
The Time Problem
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis (21.5)

The only premise that all of the precellular theories share is that it would be an extremely long time before the first bacterial cells evolved. If precellular life somehow got going, it could then conceivably begin to crank out, by some precellular process, random strings of nucleotides and amino acids, trying to luck into a gene or a protein with advantages which would lead to bacterial life. There is no evidence in life today of anything that produces huge quantities of new, random strings of nucleotides or amino acids, some of which are advantageous. But if precellular life did that, it would need lots of time to create any useful genes or proteins.
As for the Lynn Margulis statement, it's easier when you know where you came from to trace your roots than to have to guess at the starting point and work from there. Your guess better be right or who knows where it will lead.

Time we know has been in abundance on earth so anything is possible. Hopefully we have enough time to figure this out before time moves on without us.

The final conclusion is a statement about what can be garnered from many years of investigative work-

Quote:
Summary
There is no remnant or trace evidence of precellular life anywhere today. That it ever existed is entirely conjectural.
Although its emergence from nonliving matter is hard to conceive, precellular life must have appeared almost immediately.
There was almost no time for precellular life to evolve into the simplest bacterial cells.
Precellular life has never been created in a lab.
In spite of the RNA world, there is no consensus on the model for precellular life.
We said that research in the RNA world is a medium-sized industry. This research has demonstrated how exceedingly difficult it would be for living cells to originate by chance from nonliving matter in the time available on Earth. That demonstration is a valuable contribution to science. Additional research will be valuable as well. But to keep insisting that life can spontaneously emerge from nonliving chemicals in the face of the newly comprehended difficulties is puzzling. It is reminiscent of the persistent efforts of medieval alchemists to turn lead into gold.


At least we are staying consistent- who says we don't know the lessons of history as they repeat themselves over and over again.

This final statement may be an example of an outside force being a stimulus to life.

Quote:
There is another scientific explanation for the origin of life on Earth. It is that whole cells arrived here from space.
Would that be an example of an outside initial start GG?

APL- this site talks a little about that and gives references to that soup theory as well. Calls it Pre-precellular life. It also states that precellular life has never been formed in the laboroatory. I guess GG can explain it to us and tell us whether they have managed to do it since then.

It seems the more we think we know, the more we open up to find out what we don't know. Pandora's Box?

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PostPosted: Sun Feb 10, 2008 2:55 pm 
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DO.g's wrote:
Would that be an example of an outside initial start GG?
It all depends on what we wish to call our system. If it is earth, then yes it would be outside. If its the universe, then no.

Quote:
APL- this site talks a little about that and gives references to that soup theory as well. Calls it Pre-precellular life. It also states that precellular life has never been formed in the laboroatory. I guess GG can explain it to us and tell us whether they have managed to do it since then.
Weve actually almost createda whole synthetic organism.

I will say I have a few issues with your website. After reading some of the links and stuff it appears that they quote mine and like to play games with statistics. Ive learned that anytime people start playing with probability like that, its simply because they lack any real evidence to support their ideas.

What the website seems to say is that its improbable that life formed on earth (a logical fallacy right there) and then presume then that it must have came from outer space. (another fallacy) Since there is zero evidence that supports that, the notion that god created life, or even magic fairies has just as much credibility. Thats my $.02

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