Unintelligent Design

[Acriku]

This is an exciting find that I just have to post a topic about it, because it's revamping what we know of viruses to this day. Here's the article. A couple excerpts relevant to this topic:

Now, with the recent discovery of a truly monstrous virus, scientists are again casting about for how best to characterize these spectral life-forms. The new virus, officially known as Mimivirus (because it mimics a bacterium), is a creature "so bizarre," as The London Telegraph described it, "and unlike anything else seen by scientists . . . that . . . it could qualify for a new domain in the tree of life." Indeed, Mimivirus is so much more genetically complex than all previously known viruses, not to mention a number of bacteria, that it seems to call for a dramatic redrawing of the tree of life.

"This thing shows that some viruses are organisms that have an ancestor that was much more complex than they are now," says Didier Raoult, one of the leaders of the research team at the Mediterranean University in Marseille, France, that identified the virus. "We have a lot of evidence with Mimivirus that the virus phylum is at least as old as the other branches of life and that viruses were involved very early on in the evolutionary emergence of life."

That represents a radical change in thinking about life's origins: Viruses, long thought to be biology's hitchhikers, turn out to have been biology's formative force.

This is striking news, especially at a moment when the basic facts of origins and evolution seem to have fallen under a shroud. In the discussions of intelligent design, one hears a yearning for an old-fashioned creation story, in which some singular, inchoate entity stepped in to give rise to complex life-forms

[Dante]

I would be inclined to wait for more evidence and detail before breaking out the champagne. The last thing we need is for this to be another Piltdown man.

[GUNWOUNDS]

Virus particles are also theorized to be nothing more than bacterial weapons that have gone independently rogue.

Bacteria are known for competing with each other.... Penicillin was originally isolated from the Penicillium chrysogenum, A mold.  Bacteria are know for creating weapons to kill other bacteria in order to win competition for nutrients. 

Bacteria also use virus particles in some instances to destroy other bacteria.  Bacteria also exhibit defense mechanisms against virus attacks as well.... many bacteria have methylated DNA which means methyl groups (CH3) block important sites around the Bacteria's DNA due to steric hindrance.  Also some DNA have RNAses and DNases that attack virus DNA /RNA and chop it up like scissors chopping up paper.  So RNAses and DNAses are bacterial weapons too.... what are we gonna call them alive next?  Or the next ancestor? *chuckle*

This leads me to believe that virus particles are nothing more than rogue bacterial weapons that have become independant.  And this is likely the case because virus particles are nothing more than rogue pieces of DNA and DNA can easily go rogue ......as DNA is very mechanical by nature.  Almost machine-like.  And we all know machines can malfunction.

Best way to describe it would be to use terminators as an example. Mankind could build termiantors to kill other humans... but those terminators could find a way.... even if by accident.... to become rogue and independant and start killing any human.  And the fact that bacteria have defense mechanisms would lead one to believe that there is indeed a bacterial war raging, and it seems some viral weapon machines have gone awry.

This article you linked to seems very "sensational" and the author sounds a bit "too excited"  so its as if they are trying to manipulate the data and situation in order to get people to be excited to read this article.  Which is understandable since they want to sell copies.  But calling it a "monstrous discovery"  and "mother cell of all life"  and "evolutionary discovery of the millenium"  is pretty silly. They found some viral DNA that does some fancy stuff... big deal.  It just means its a fancy weapon.  Sorta like the laser guided missiles we humans make to fly into the windows of buildings.  Its just on a microscopic machinery scale.

Guns

[GUNWOUNDS]

Also wanted to add that viral DNA already mimics bacterial cells because it takes over the cell's machinery when it attacks a cell... bascially overriding the cell's DNA and making all the cellular machinery produce vrius DNA and capsules for futher distrubution.

THe reason why cells had to have come before virus particles is because DNA/RNA requires certain things to replicate.... it needs transporter molecules (tRNA) it needs template molecules (mRNA) , it needs special proteins to regulate its expression. It needs polymerase molecules to replicate it and repair it (DNA Polymerase)  (RNA Polymerase).

Now only cells contain these complex and wonderful micromachines.  A viral strand of DNA sitting out in some mud isnt going to have this.  And RNA and DNA will degrade quickly when not taken care of.  Therefore an enclosed cellular membrane with cytoplasm and tons of micromachines acting as room service to the DNA/RNA is the ideal situation for genetic replication and maintenance.

Therefore it only makes sense that the housing the virus is enclosed in has to be originated from a cell.  As well as the DNA/RNA itself.  IF a viral particle is dpeendant upon bacteria for parts and materials it only makes sense that virus particle originated from bacteria.  And since viral particles are more mechanical and weapon-like than they are "alive" it only makes sense that they are bacterial weapons gone awry.

They state that Virus particles can cause mutations in bacterial DNA and that Viral particles are evolution's primary force.  That was something i rememebr a professor saying 4 years ago.  I know why they think that......Its becuz a virus attacking a cell can integrate itself into the DNA but fail to kill the cell.... and so the viral DNA sequence is encoded inbetween some bacterial DNA which will carry over to new generations ....because when a bacterial cell replicates itself it will replicate the inserted viral DNA.

This could lead to farther distanced exons and introns which could change expression of already existing genes which could produce less or more proteins product than usual.  However, it is also theorized that much of the DNA that is inserted by viral particles is miniscule and either is unused or causes fatal effects.

Therefore it is unlikely that virus particles are responsible for something as complex as a human being.  In terms of DNA.... it is so sensitive that most mutations are fatal to an organism.  "Wonderful positive" mutations are incredibly unlikely.  Especially multiple mutations.  Probability is so stacked against you... mutations will most likely result in failure to replicate your DNA or uncontrollable replication as in cancer.  And multiple mutations will only damn you further.

Hold a bacterial colony under UV light for 5 seconds and they become so weak due to their DNA being mutated that they die in a short period of time due to replication failure.  Hold them under UV light for 30 seconds and immediate death results due to total DNA breakdown.  Microbiology 101.

We didnt get here by mutation.  If anything our DNA is getting shittier by the decade. Due to constant UV exposure, Mutagen ingestion, carcinogen ingenstion, carcinogen inhalation.  We are degrading... we arent getting better.  Mutation as a evolutionary force that created man from primates is almost unbelievable. Its like believing the John Travolta Movie "Phenomena" where he gets a brain tumor that has positive effects on him and gives him super telekinetic powers and enhanced intelligence.  Unlikely.

Guns.

[Dante]

DNA self-repairs itself as you well know Gunwounds. If it constantly deteriorated then we wouldn't even be here, and the question of how we got here would hardly be important. And mutation as an evolutionary force isn't such a wacky idea, but it depends on the mutation. Certainly those caused by radiation wouldn't be candidates, but genetic mutations that occur by accident have something to say for themselves. Sickle cells affording resistance to Malaria, for example. A random mutation that has flourished due to enviromental factors that favour it.

I haven't looked into this virus thing, but I plan to at a later date. I like viruses. There is another theory regarding bacterial - rather than viral - effect on (and possiboe creation of) animal and plant evolution, but I don't have time to go into it right now. You probably know about it already.

More when I don't have meetings to attend.

[GUNWOUNDS]

DNA self-repairs itself as you well know Gunwounds. If it constantly deteriorated then we wouldn't even be here,

Ah that is a misunderstanding on your part.... it "self repairs" but that is a misnomer.  DNA polymerase I performs repairs WITH the presence of complex nucleotides ALREADY existing within the cytoplasm of the cell.  That is what we call DNA "repairing itself".  I hope you can see how that is a misnomer... as the DNA is having many tiny micromachines that are present ONLY in a cell and it really isnt repairing itself all by itself..

And we incur DNA errors every 1 billionth replication which happens quite offten seeing as how we have billions of cells.  And to be honest our DNA is constantly degrading and mental retardation is increasing at an alarming rate.  You say that if our DNA was degrading we wouldnt be here anymore.... thats not true.... it takes time for us to "Disappear".  Cancer, mental retardation, birth defects, etc, etc..... errors are constantly building up in us and no amount of "DNA polymerase I" repair activity is going to change that. It will take a very long time for it to wipe out the human race entirely. But due to genetic engineering we will probably find a way to reverse genetic degradation.

Oh and btw sickle cell anemia may help someone survive malaria but those people are still genetically defective as they are more prone to heart problems, health problems in general, and even Hemorrhage.  Another symptom is simple shortening of their lifespan.  Not necessarily a positive mutation IMO, despite the malaria resistance.  Oh and environmental factors dont help sickle cell anemia victims "flourish" ... they would still have their shortened lifespan and hemorrhaging and anemic blood all the same, even if they were in an area where there is no malaria. So the environment is a moot point here, and the malaria resistance is merely a coincidental irrelevant benefit.

My point is that mutations will usually be defective rather than beneficial due to plain probability, and that compounded mutations will only damn your chances  further, make your life shorter, or kill you outright.  Having a positive mutation that is akin to John Travolta's "Phenomena" where he gets super powers and super intelligence from a tumor in his brain is pretty unlikely. And to have a tumor or DNA mutation give a monkey the capacity to create the English Language, build a skyscraper, and land on the moon is outright rediculous, IMO.  But thats just me.

Guns

[Acriku]

This leads me to believe that virus particles are nothing more than rogue bacterial weapons that have become independant.  And this is likely the case because virus particles are nothing more than rogue pieces of DNA and DNA can easily go rogue ......as DNA is very mechanical by nature.  Almost machine-like.  And we all know machines can malfunction.

Which would not be the case if their genetic material goes back before other branches of life, which was what the article was making note of, something one would have seen if they had read it. This discovery brings into question just what you "are lead to believe" about viruses. That was a major point of the discovery.

This article you linked to seems very "sensational" and the author sounds a bit "too excited"  so its as if they are trying to manipulate the data and situation in order to get people to be excited to read this article.  Which is understandable since they want to sell copies.  But calling it a "monstrous discovery"  and "mother cell of all life"  and "evolutionary discovery of the millenium"  is pretty silly. They found some viral DNA that does some fancy stuff... big deal.  It just means its a fancy weapon.  Sorta like the laser guided missiles we humans make to fly into the windows of buildings.  Its just on a microscopic machinery scale.

Big deal? Have you read the article? This will lead scientists into revamping the branches of life and change what we think is alive, or dead. Viruses have seemed to be chemical in nature, which they do seem to do, but with the mimivirus that distinction is becoming less and less clear and with this discovery viruses will get a biological look as well as chemical. Your attempts to downplay what is to be very exciting stuff for evolutionary biology (and even other fields) is just what one would expect from a creationist (albeit not on my list of what were possible reactions).

[Acriku]

Oh and btw sickle cell anemia may help someone survive malaria but those people are still genetically defective as they are more prone to heart problems, health problems in general, and even Hemorrhage.  Another symptom is simple shortening of their lifespan.  Not necessarily a positive mutation IMO, despite the malaria resistance.  Oh and environmental factors dont help sickle cell anemia victims "flourish" ... they would still have their shortened lifespan and hemorrhaging and anemic blood all the same, even if they were in an area where there is no malaria. So the environment is a moot point here, and the malaria resistance is merely a coincidental irrelevant benefit.

The environment is not a moot point, it's actually a great factor in why sickle cell anemia is widespread among African-Americans. In Africa, malaria was a constant threat, and just as one would see in a naturally selected population we have a large population of Africans with sickle cell anemia because it protects against malaria. You wouldn't normally see this in environments where malaria wasn't a threat. This is natural selection.

My point is that mutations will usually be defective rather than beneficial due to plain probability, and that compounded mutations will only damn your chances  further, make your life shorter, or kill you outright.  Having a positive mutation that is akin to John Travolta's "Phenomena" where he gets super powers and super intelligence from a tumor in his brain is pretty unlikely. And to have a tumor or DNA mutation give a monkey the capacity to create the English Language, build a skyscraper, and land on the moon is outright rediculous, IMO.  But thats just me.

Guns

Outright rediculous for the largely uninformed, sure. This just shows how little you have of an appreciation for the time duration and amount of mutations involved to go from an ancestor similar to that of an ape to what we are today. Which is fine by me, because it discredits you in an easy fashion. Also, mutations are not inherently defective or beneficial, it all depends largely on the environment. Compounded mutations that were compounded in a naturally selected population would not damn your chances further necessarily, since they've already been naturally selected to survive with the genes they had prior to the mutations.

[Dante]

Ah that is a misunderstanding on your part.... it "self repairs" but that is a misnomer.  DNA polymerase I performs repairs WITH the presence of complex nucleotides ALREADY existing within the cytoplasm of the cell.  That is what we call DNA "repairing itself".  I hope you can see how that is a misnomer... as the DNA is having many tiny micromachines that are present ONLY in a cell and it really isnt repairing itself all by itself..

I do know that. You said:

We didnt get here by mutation.  If anything our DNA is getting shittier by the decade. Due to constant UV exposure, Mutagen ingestion, carcinogen ingenstion, carcinogen inhalation.  We are degrading... we arent getting better.  Mutation as a evolutionary force that created man from primates is almost unbelievable.

This implies that you were talking about humans, which are made out of cells. And our DNA has mechanisms with which to repair itself, thus for all intents and purposes, it is self-repairing. Just because I choose to simplify doesn't mean that I'm unaware of the more complex explanation.

And we incur DNA errors every 1 billionth replication which happens quite offten seeing as how we have billions of cells.  And to be honest our DNA is constantly degrading and mental retardation is increasing at an alarming rate.  You say that if our DNA was degrading we wouldnt be here anymore.... thats not true.... it takes time for us to "Disappear".  Cancer, mental retardation, birth defects, etc, etc..... errors are constantly building up in us and no amount of "DNA polymerase I" repair activity is going to change that. It will take a very long time for it to wipe out the human race entirely. But due to genetic engineering we will probably find a way to reverse genetic degradation.

That's a very odd attitude for a creationist to take. Nevermind...

The human race has existed for well over five thousand years. If DNA degradation was going to end us, it would have done so by now. And even outside our species, there are others such as sharks, starfish, rats, that have remained virtually unchanged for millions of years. Their DNA shows no signs of a slow-motion implosion.

Mental conditions and birth defects may be on the increase due to outside factors, but I would also remember that the population of the world is increasing at an exponential rate (far too fast in fact). The percentage of birth defects may be the same as ever, or only slightly increased, but the number of individuals will drastically rise because that is what the population is doing.

It could even be argued that we are only seeing such an increase now because it is only now that such individuals are surviving long enough to be recorded.

Oh and btw sickle cell anemia may help someone survive malaria but those people are still genetically defective as they are more prone to heart problems, health problems in general, and even Hemorrhage.  Another symptom is simple shortening of their lifespan.  Not necessarily a positive mutation IMO, despite the malaria resistance.  Oh and environmental factors dont help sickle cell anemia victims "flourish" ... they would still have their shortened lifespan and hemorrhaging and anemic blood all the same, even if they were in an area where there is no malaria. So the environment is a moot point here, and the malaria resistance is merely a coincidental irrelevant benefit.

You missed the point. Sickle cell anaemia is not a beneficial disease, that much is obvious. And non-beneficial mutations have a tendancy to die out. That's part of how evolution works. Beneficial mutations give an individual an edge over their fellows, thus passing on the genotype; degrading mutations give it a disadvantage and thus the genotype dies out. However, sickle cell anaemia grants increased resistance to malaria, and so in areas where malaria is endemic it will be genetically advantageous to have it, despite the negative symptoms.

To put it another way, if there is an outbreak of malaria in a village and two thirds of the survivors are only alive because they had sickle cell anaemia, then whose genes are most likely to be passed on? Thus the genotype flourishes.

Conversely, in areas where malaria is not a problem, those with sickle cell anaemia will certainly be at a disadvantage and are far less likely to pass on their genes. If you look at maps showing incidence of malaria and incidence of sickle cell anaemia, there are some very close correlations.

My point is that mutations will usually be defective rather than beneficial due to plain probability, and that compounded mutations will only damn your chances  further, make your life shorter, or kill you outright. Having a positive mutation that is akin to John Travolta's "Phenomena" where he gets super powers and super intelligence from a tumor in his brain is pretty unlikely. And to have a tumor or DNA mutation give a monkey the capacity to create the English Language, build a skyscraper, and land on the moon is outright rediculous, IMO. But thats just me.

Tumours aren't exactly genetic mutations.

Anyway, whether a mutation is positive or negative can depend on enviroment. Sickle cells prove that. Ordinarily negative, but sometimes positive. I think there's a similar relationship between Down's Syndrome and typhoid, but I'd have to double check that one to be sure.

Now, on to the symbiosis theory. Is that what it's called? No, Endosymbiont. That's it.

Basically, the theory argues that animal and plant cells were originally bacteria. Some of it makes a lot of sense. The original theory was dreamed up by Mereschkovsky in 1905, and stated that mitochondria were in fact symbiotic bacteria that could be cultured outside of cells. That idea was laughed out of the establishment of course. But later on, there may be a grain of truth in there.

For a start, mitochondria and chloroplasts (the two organelles that are the focus for the theory) are about the same size as bacteria. They have their own DNA, which is circular as bacterial DNA is. They have their own ribosomes, and protein synthesis mechanisms. And not only that, but mechanisms similar to those in bacteria. Their RNA polymerase is inhibited by ripamfcin, as bacterial RNA polymerase is, but nuclear RNA polymerase is not. Chloroplast and mitochonrial ribosomes are smaller (70s) than those in the cytoplasm (80s), about the same size as bacterial ribosomes. Nucleotide base sequences in bacterial and organelle ribosomal RNA are more similar to each other than to cytoplasmic ribosomes.

Drugs such as chloramphenicol block protein synthesis in bacteria but not that in the cytoplasm of animal or plant cells. But the same drug inhibits mitochondrial and chloroplast protein synthesis. Conversely, there are drugs that inhibit cytoplasmic protein synthesis but not that of bacteria or the organelles (cycloheximide).

At the most basic level, the Endosymbiont theory suggests that chloroplasts (and the accompanying chromoplasts, amyloplsts, etc) and mitochondria were once seperate bacteria that were taken in by larger bacteria, developing a symbiotic relationship. The benefits to both parties are obvious. Taking up a chloroplast allows a cell to gain sugars through photosynthesis, while taking up mitochondria provides a massive energy boost (the larger cell would only have been capable of anaerobic respiration, that found in the cytoplasm today). The absorbed bacteria would gain extra protection, and a constant supply of food or materials. After all if you devote all your resources to making energy or photosynthesising then it makes sense to team up with someone that has a more efficient method of gathering supplies. There are in fact species of bacteria that have ATP synthesising complexes grouped in folds of their plasma membrane, and from there it isn't such a great leap to the cristae of mitochondria. The ancestral chloroplast could well have been an early cyanobacterium.

The original taking in might have been as undigested food or even as parasites on the host. Personally I find the latter more likely, as the former would have required the larger prokaryote to lose its cell wall in order to 'eat' smaller cells.

Of course the bacterial cells would have lost some parts of themselves over time, pieces that the larger host could handle more efficiently. At the same time the host would have lost pieces, and developed differently. Eventually it became impossible for the smaller organisms to survive apart from each other. It may be that the double membrane around chloroplasts and mitochondria is in fact the remains of the two plasma membranes (one from the host, the other from the parasite/food) from long ago.

Er... yeah. I actually have many many pages of notes on this topic (including stuff on the RER, Golgi Body, etc), but I'll save myself the effort for now and just say that it's an interesting theory with a lot to say for it. If true, it would make bacteria the big movers and shakers behind evolution, not viruses. And if true, then viral influence on evolution might not be so far fetched as some might imagine.

[GUNWOUNDS]

Which would not be the case if their genetic material goes back before other branches of life, which was what the article was making note of

"Goes back before other branches of life" ? ... are you serious?.... and just how will they determine that?  YOu cant look at a piece of DNA and say.... "ohh this pre-dates other DNA".  SOunds like a whole lot of assumptions and fancy stories.

I will repeat.... environment has nothing to do with sickle cell anemia.... a person with sickle cell anemia will live the same amount of years regardless of whether or not they are in an environment with malaria. Sickle cell anemia is NOT a fatal defect...this means that Africans would have developed sickle cell anemia and would have lived with it and have proliferated it REGARDLESS of malaria being in the area.  Just as there are people who have all kinds of genetic problems who dont live in malaria infested regions.  Their genetic problems are just that... genetic problems has nothing to do with their environment.  

You say selected mutations over time selecting for different environments etc, etc, are what turned us from apes to men.... yea except your example of having sickle cell anemia shortens your lifespan.... so lets give them another and another and another mutation and lets watch their lifespan get smaller and smaller and smaller. Hmmmm seeems like our mutations are making us worse not better.  Oops.

Outright rediculous for the largely uninformed, sure. This just shows how little you have of an appreciation for the time duration and amount of mutations involved to go from an ancestor similar to that of an ape to what we are today. Which is fine by me, because it discredits you in an easy fashion. Also, mutations are not inherently defective or beneficial, it all depends largely on the environment. Compounded mutations that were compounded in a naturally selected population would not damn your chances further necessarily, since they've already been naturally selected to survive with the genes they had prior to the mutations.

Sounds like a fancy story to me.... oh wait... mutations arent inherently beneficial or defective?  WRONG!.  Mutations can be immediately fatal, neutral, or positive.  Most of the time mutations are fatal, then comes neutral , and the least probable is positive.  If a mutation occurs where your cells dont produce DNA polymerase III then you cant replicate your DNA... whoops guess thats a fatal mutation.  And its hard to have beneficial mutations because the gentic code is so sensitive that anything screwing with it is bound to cause problems ... not benefits.  Why do you think one cancer tumor usually ends a person's life?  Becuase mutations are usually bad and our bodies are sensitive to any changes.

You say i dont respect the time and duration it took for us to become men from apes... but YOU dont respect  what it means to have a mutation occur in your body.  You think they are just wonderful little changes that turn creatures into other creatures... when in actuality, mutations are destructive, degrading mechanisms and through time and duration you are going to have more and more errors and problems. Logically we shouldnt have primitive organisms suffering through millions of years of UV radiation, carcinogens, toxins, viral attacks, and having their DNA degraded, chock full of errors and then turn into a complex creature such as a monkey and then having that monkey subjected to the same degrading guantlet only to become the most advanced creature the planet has known, sounds like a fancy story to me.  It makes more sense for organisms to degrade to the point of immortal cancer-ridden cell blobs that resist radiation and chemotherapy, like we see today.  

Guns

[GUNWOUNDS]

I do know that. You said: This implies that you were talking about humans, which are made out of cells. And our DNA has mechanisms with which to repair itself, thus for all intents and purposes, it is self-repairing. Just because I choose to simplify doesn't mean that I'm unaware of the more complex explanation.

That's a very odd attitude for a creationist to take. Nevermind...

The human race has existed for well over five thousand years. If DNA degradation was going to end us, it would have done so by now. And even outside our species, there are others such as sharks, starfish, rats, that have remained virtually unchanged for millions of years. Their DNA shows no signs of a slow-motion implosion.

Mental conditions and birth defects may be on the increase due to outside factors, but I would also remember that the population of the world is increasing at an exponential rate (far too fast in fact). The percentage of birth defects may be the same as ever, or only slightly increased, but the number of individuals will drastically rise because that is what the population is doing.

It could even be argued that we are only seeing such an increase now because it is only now that such individuals are surviving long enough to be recorded.

You missed the point. Sickle cell anaemia is not a beneficial disease, that much is obvious. And non-beneficial mutations have a tendancy to die out. That's part of how evolution works. Beneficial mutations give an individual an edge over their fellows, thus passing on the genotype; degrading mutations give it a disadvantage and thus the genotype dies out. However, sickle cell anaemia grants increased resistance to malaria, and so in areas where malaria is endemic it will be genetically advantageous to have it, despite the negative symptoms.

To put it another way, if there is an outbreak of malaria in a village and two thirds of the survivors are only alive because they had sickle cell anaemia, then whose genes are most likely to be passed on? Thus the genotype flourishes.

Conversely, in areas where malaria is not a problem, those with sickle cell anaemia will certainly be at a disadvantage and are far less likely to pass on their genes. If you look at maps showing incidence of malaria and incidence of sickle cell anaemia, there are some very close correlations.

Tumours aren't exactly genetic mutations.

Anyway, whether a mutation is positive or negative can depend on enviroment. Sickle cells prove that. Ordinarily negative, but sometimes positive. I think there's a similar relationship between Down's Syndrome and typhoid, but I'd have to double check that one to be sure.

Now, on to the symbiosis theory. Is that what it's called? No, Endosymbiont. That's it.

Basically, the theory argues that animal and plant cells were originally bacteria. Some of it makes a lot of sense. The original theory was dreamed up by Mereschkovsky in 1905, and stated that mitochondria were in fact symbiotic bacteria that could be cultured outside of cells. That idea was laughed out of the establishment of course. But later on, there may be a grain of truth in there.

For a start, mitochondria and chloroplasts (the two organelles that are the focus for the theory) are about the same size as bacteria. They have their own DNA, which is circular as bacterial DNA is. They have their own ribosomes, and protein synthesis mechanisms. And not only that, but mechanisms similar to those in bacteria. Their RNA polymerase is inhibited by ripamfcin, as bacterial RNA polymerase is, but nuclear RNA polymerase is not. Chloroplast and mitochonrial ribosomes are smaller (70s) than those in the cytoplasm (80s), about the same size as bacterial ribosomes. Nucleotide base sequences in bacterial and organelle ribosomal RNA are more similar to each other than to cytoplasmic ribosomes.

Drugs such as chloramphenicol block protein synthesis in bacteria but not that in the cytoplasm of animal or plant cells. But the same drug inhibits mitochondrial and chloroplast protein synthesis. Conversely, there are drugs that inhibit cytoplasmic protein synthesis but not that of bacteria or the organelles (cycloheximide).

At the most basic level, the Endosymbiont theory suggests that chloroplasts (and the accompanying chromoplasts, amyloplsts, etc) and mitochondria were once seperate bacteria that were taken in by larger bacteria, developing a symbiotic relationship. The benefits to both parties are obvious. Taking up a chloroplast allows a cell to gain sugars through photosynthesis, while taking up mitochondria provides a massive energy boost (the larger cell would only have been capable of anaerobic respiration, that found in the cytoplasm today). The absorbed bacteria would gain extra protection, and a constant supply of food or materials. After all if you devote all your resources to making energy or photosynthesising then it makes sense to team up with someone that has a more efficient method of gathering supplies. There are in fact species of bacteria that have ATP synthesising complexes grouped in folds of their plasma membrane, and from there it isn't such a great leap to the cristae of mitochondria. The ancestral chloroplast could well have been an early cyanobacterium.

The original taking in might have been as undigested food or even as parasites on the host. Personally I find the latter more likely, as the former would have required the larger prokaryote to lose its cell wall in order to 'eat' smaller cells.

Of course the bacterial cells would have lost some parts of themselves over time, pieces that the larger host could handle more efficiently. At the same time the host would have lost pieces, and developed differently. Eventually it became impossible for the smaller organisms to survive apart from each other. It may be that the double membrane around chloroplasts and mitochondria is in fact the remains of the two plasma membranes (one from the host, the other from the parasite/food) from long ago.

Er... yeah. I actually have many many pages of notes on this topic (including stuff on the RER, Golgi Body, etc), but I'll save myself the effort for now and just say that it's an interesting theory with a lot to say for it. If true, it would make bacteria the big movers and shakers behind evolution, not viruses. And if true, then viral influence on evolution might not be so far fetched as some might imagine.

  Yes but get this....The endosymbionts do show genetic degradation. Genome sequencing reveals that obligate bacterial endosymbionts of insects have among the smallest of known bacterial genomes and have lost many genes that are commonly found in other bacteria. some say the genes are not needed in the environment of the host insect cell, but another theory is that since the endosymbionts are maternally transmitted and have no opportunity to exchange genes with other bacteria, it is more difficult to keep good genes in all individuals in a population of these endosymbionts. Scientists want to understand how bacteria with severely depleted genomes are able to survive.

You see... even with Endosymbiosis there is genome degradation.  Also even if Endosymbiosis was how eukaryotes were formed.... that doesnt mean it has limitless potential.  My car has a limit... i can floor it but i will never break out into warp speed and fly off.  And endosymbiosis doesnt mean that advance multicellular creatures with organ systems such as humans would arise just because an insect allows a bacterium to live inside it or because a plant cell absorbs another cell.  Its like saying that because we have shown how gasoline engines can work that one day we will have a warp engine.  Pretty unlikely.  Biology just like physics has limits.

Guns

[Dante]

The Endosymbiont theory was indended as a seperate point, related to the original claims regarding viral effect on evolution. For the responses to your post, look at the bits of my post specifically related to them. Quoting the whole thing just looks... ugly. Like a carefully laid pattern being squashed together.

[Dude_Doc]

This is just a sidenote, but I have to side with the theologists. If "intelligent design" is true, then I believe things created before man somehow fits into the whole creation. It isn't like this "new" bacteria is going to change the life of those who live in poverty, or stop war.

I think there is a bigger "question" too, in the same sence as this thread, but different. Our planet has a moon, which is a must because it keeps our planet stable, otherwise we would have different seasons twice a month (winter today, 60+ tomorrow etc). We also know how to use methane as a fuel - thus we have Titan, the moon of Saturn, covered in methane. We could use it to power all of earth for millions of years to come, or even better, use it as fuel to reach other places in our galaxy. Coincidence or designed for us?

I think it depends on how you look at it...

[Dante]

Sure, I can just see the logic.

GOD: Yes, these people are going to need lots of methane to help them power things. I know! I'll create a whole lot of it for them and put it on a planetoid a few million miles away. Genius!

Pff. You might as well argue that plants exist for the use of vegetarians or that we wouldn't have summer without the sun. These are nonsensical statements based on the fact that some things exist in a pattern. 'Oo, cows eat grass. Grass must have been created for cows!'

Also, seasons are controlled by the slight tilting of the Earth on its axis. Moon has little to no effect on that. And the bacterium isn't newly discovered, the virus is.

[Dunenewt]

When I saw the title of this thread, I assumed it was about the Fiat Multipla...

[Dragoon Knight]

DEAR GOD, I hate that car.

[GUNWOUNDS]

Thats pretty funny.

[GUNWOUNDS]

Sure, I can just see the logic.

GOD: Yes, these people are going to need lots of methane to help them power things. I know! I'll create a whole lot of it for them and put it on a planetoid a few million miles away. Genius!

Pff. You might as well argue that plants exist for the use of vegetarians or that we wouldn't have summer without the sun. These are nonsensical statements based on the fact that some things exist in a pattern. 'Oo, cows eat grass. Grass must have been created for cows!'

Also, seasons are controlled by the slight tilting of the Earth on its axis. Moon has little to no effect on that. And the bacterium isn't newly discovered, the virus is.

Well otherman has a point about a few things.... there are several things in this solar system that make it appear "pre-made" ... The solar system has to be hospitable not just the planet.  If the solar system has two suns it will wreak havok on the ocean tides.  If the solar system doesnt have a large gas giant like jupiter to absorb and deflect comets and meteors the home planet will get hit by asteroids, comets, whatever 1000% more.  And since the dinosaurs were believed to have died by a comet... then we should be very thankful for having a deflector planet like jupiter.

There are so many other things needed for a hospitable and life sustaining solar system and i dont have time to list them all.  Luminance of the sun and the rate of solar eruptions is another.  If these factors are too high then too much luminance and UV would penetrate the planet.  Also the sun has to be the right age.. not too old not to young... also you need orbit stabilizing planets like saturn and jupiter.  Without them our orbit would become chaotic.

And many of these factors i described eliminates most solar systems from being able to sustain life. Thats where the trillionth of a trillionth of a trillionth of a trillionth of a percent comes in. Especially in regards to intelligent life. 

Our Solar System  was made perfectly with orbit stabilizer planets, comet deflector/absorber planets, and a sun and earth that are the right age.  Either this whole thing was carefully put together or we are all incredibly lucky.

[Acriku]

"Goes back before other branches of life" ? ... are you serious?.... and just how will they determine that?  YOu cant look at a piece of DNA and say.... "ohh this pre-dates other DNA".  SOunds like a whole lot of assumptions and fancy stories.

Hey pot, it's me: Kettle! Please gunwounds, you of all people should not be talking about fancy stories and a lot of assumptions. In any case, this is from the article:

"This thing shows that some viruses are organisms that have an ancestor that was much more complex than they are now," says Didier Raoult, one of the leaders of the research team at the Mediterranean University in Marseille, France, that identified the virus. "We have a lot of evidence with Mimivirus that the virus phylum is at least as old as the other branches of life and that viruses were involved very early on in the evolutionary emergence of life."

Am I a microbiologist or a viral chemist? No, so I wouldn't even understand most of the evidence behind this assertion. But, I trust in other scholars of those areas to credit or discredit the supposed evidence. We will find out soon enough.

I will repeat.... environment has nothing to do with sickle cell anemia.... a person with sickle cell anemia will live the same amount of years regardless of whether or not they are in an environment with malaria.

Um, a shorter life does not matter much in the big scale of things if the organism can live past fertility and be able to produce organisms for the species to live on. Populations not able to fight against malaria will not live past fertility if they receive it early on (symptoms showing as soon as 7 days, or as long as 21 days). Being quite fatal, malaria could very well stop a population from growing or sustaining itself. But, if the population has a certain condition known as sickle cell anemia, it has an advantage over the other population and can sustain itself and even grow. This is a classic example of the environment playing a vital role in the benefits of certain mutations. My roommate high on pot can understand this.

Sickle cell anemia is NOT a fatal defect...this means that Africans would have developed sickle cell anemia and would have lived with it and have proliferated it REGARDLESS of malaria being in the area.  Just as there are people who have all kinds of genetic problems who dont live in malaria infested regions.  Their genetic problems are just that... genetic problems has nothing to do with their environment. 

Just as well, having that condition gives an advantage to the population with it over a population without it, and can grow far past it (being able to gather more resources, reaching age of fertility, etc).

Come on man, don't be stubborn. This isn't difficult.

You say selected mutations over time selecting for different environments etc, etc, are what turned us from apes to men.... yea except your example of having sickle cell anemia shortens your lifespan.... so lets give them another and another and another mutation and lets watch their lifespan get smaller and smaller and smaller. Hmmmm seeems like our mutations are making us worse not better.  Oops.

Once again, it does not matter if the life of an organism is shortened, it only matters if the organism lives to its fertility age or not. Once an organism has reproduced, in the coldest perspective on this matter the organism has no further use in the large scale. Oops. Did I just make you wrong?

You say i dont respect the time and duration it took for us to become men from apes... but YOU dont respect  what it means to have a mutation occur in your body.  You think they are just wonderful little changes that turn creatures into other creatures... when in actuality, mutations are destructive, degrading mechanisms and through time and duration you are going to have more and more errors and problems. Logically we shouldnt have primitive organisms suffering through millions of years of UV radiation, carcinogens, toxins, viral attacks, and having their DNA degraded, chock full of errors and then turn into a complex creature such as a monkey and then having that monkey subjected to the same degrading guantlet only to become the most advanced creature the planet has known, sounds like a fancy story to me.  It makes more sense for organisms to degrade to the point of immortal cancer-ridden cell blobs that resist radiation and chemotherapy, like we see today. 

Guns

Wonderful little changes? After I just said mutations' benefits can only be determined in the context of an environment? Good lord man, are you willingly ignoring what I am saying? Are you going off of what ever persona of me you have in mind? In any case, I don't much care if you think it's just a fancy story. That's your poorly misguided, uninformed, and ignorant opinion. But it is yours and I will die for your right to say it (actually not really, but saying it puts me into a patriotic light, good for publicity you know  ;)).

[Acriku]

Well otherman has a point about a few things.... there are several things in this solar system that make it appear "pre-made" ... The solar system has to be hospitable not just the planet.  If the solar system has two suns it will wreak havok on the ocean tides.  If the solar system doesnt have a large gas giant like jupiter to absorb and deflect comets and meteors the home planet will get hit by asteroids, comets, whatever 1000% more.  And since the dinosaurs were believed to have died by a comet... then we should be very thankful for having a deflector planet like jupiter.

There are so many other things needed for a hospitable and life sustaining solar system and i dont have time to list them all.  Luminance of the sun and the rate of solar eruptions is another.  If these factors are too high then too much luminance and UV would penetrate the planet.  Also the sun has to be the right age.. not too old not to young... also you need orbit stabilizing planets like saturn and jupiter.  Without them our orbit would become chaotic.

And many of these factors i described eliminates most solar systems from being able to sustain life. Thats where the trillionth of a trillionth of a trillionth of a trillionth of a percent comes in. Especially in regards to intelligent life. 

Our Solar System  was made perfectly with orbit stabilizer planets, comet deflector/absorber planets, and a sun and earth that are the right age.  Either this whole thing was carefully put together or we are all incredibly lucky.

Yes, well over billions of years life had quite a bit of time to figure itself out. If it was ever possible, where ever life began and later evolved into rational beings, they would be thinking the same thing you are: are we lucky that life found a way against so high of odds, or is there something bigger going on?

Reminds me of this analogy: If I hit a golf ball, out of all the billions of blades of grass that lay on a field, it's got to hit at least one of them. But you could turn it around and say: wow! out of the billions of blades of grass that lay on this field, the golf ball luckily hit this one! Is this luck or is there something bigger at work here? I mean, consider the odds of the ball hitting this one blade! Sound familiar?

[GUNWOUNDS]

Acriku: Hey pot, it's me: Kettle! Please gunwounds, you of all people should not be talking about fancy stories and a lot of assumptions. In any case, this is from the article:

Am I a microbiologist or a viral chemist? No, so I wouldn't even understand most of the evidence behind this assertion. But, I trust in other scholars of those areas to credit or discredit the supposed evidence. We will find out soon enough.

Gunwounds:  Touchy arent you?  Just testing you to see how you react to the comment "Fancy story".  You met my expectations.  Nice taking science on authority..... so basically they could publish anything and you would believe it?  I have seen professors trying to squeeze a dissertation out because of time constraints or tenure reasons or becuz someone needed to graduate.  You know what... science is very political and tainted at times and sensationalism and opinions often go unfiltered.  So dont get too excited ok buddy?  The "i love science !!!11111"  made me chuckle.

Acriku: Um, a shorter life does not matter much in the big scale of things if the organism can live past fertility and be able to produce organisms for the species to live on.

Gunwounds:  Yea thats great... my point is that mutations do have a negative effect on lifespan, which can ultimately have an effect on reaching "age of fertility".  Sure sickle cell anemia isnt a dangerous enough mutation to shorten the lifespan to the point of stopping you from reproducing, however the point is that if you keep compounding mutations that damage your organs, restricts oxygen absorbtion (bad for sperm production), shorten your lifespan (bad for trying to reach age of fertility), and cause internal bleeding (low chance of successful births), etc, you will essentially end up with up with a creature that will degrade to the point of possibly not being able to reach an age of fertility or carrying on a productive community as complex creatures with long gestation periods need a suitable environment to survive in during the pregnancy and then the young need to be raised to age of fertility.  Its a little more complicated then just bumping and grinding.  So you actually need to go further than the age of fertility especially if parenting is needed.  Whoops forgot about that huh? 

Acriku:  Once again, it does not matter if the life of an organism is shortened, it only matters if the organism lives to its fertility age or not. Once an organism has reproduced, in the coldest perspective on this matter the organism has no further use in the large scale. Oops. Did I just make you wrong?

Gunwounds:  No not really, as i said before ... as the organism gets more complex, parenting or even community structure is needed so i guess only bumping and grinding isnt sufficient.  Ooops did i just make you wrong? (Rhetorical question)

Acriku:  Wonderful little changes? After I just said mutations' benefits can only be determined in the context of an environment?  <Snip [unnecessary drama] >

Gunwounds:  Uh? What? Oh you were saying?  Anything that degrades or shortens life is negative IMO.  I am referring to the human race (or any organism) in general.  Sure Sickle Cell anemia may help africans resist malaria... but what if the same sickle cell anemia causes the entire african population to die out 1,000 years later due to it combining with some other mutation defects to make it lethal at birth or cause sterility?  You have to look Big Picture in this situation when you are talking billions of years of compounding mutations... if the mutations are generally destructive and degrading (which due to probability they are) to the organism then it will increase the chances of the organism ending up extinct.

Imagine people who are lactose intolerant and their genes do not code for the enzyme that breaks down lactose sugar.  What if the negative mutations compounded and they obtained similar defects and ended up not being able to digest any sugars (frustose, glucose, sucrose) and ending up starving shortly after birth?  How is that mutation not negative?  How is that situational?  I'll stop asking rhetorical questions cause I hope by now you understand.

[Acriku]

Gunwounds:  Touchy arent you?  Just testing you to see how you react to the comment "Fancy story".  You met my expectations.  Nice taking science on authority..... so basically they could publish anything and you would believe it?  I have seen professors trying to squeeze a dissertation out because of time constraints or tenure reasons or becuz someone needed to graduate.  You know what... science is very political and tainted at times and sensationalism and opinions often go unfiltered.  So dont get too excited ok buddy?  The "i love science !!!11111"  made me chuckle.

Yes, I get overexcited sometimes, but that's only because discovery is a wonderful thing. Science is a wonderful thing. The fact that that made you chuckle is odd, considering how you're supposedly a "scientist."

Gunwounds: Yea thats great... my point is that mutations do have a negative effect on lifespan, which can ultimately have an effect on reaching "age of fertility".  Sure sickle cell anemia isnt a dangerous enough mutation to shorten the lifespan to the point of stopping you from reproducing, however the point is that if you keep compounding mutations that damage your organs, restricts oxygen absorbtion (bad for sperm production), shorten your lifespan (bad for trying to reach age of fertility), and cause internal bleeding (low chance of successful births), etc, you will essentially end up with up with a creature that will degrade to the point of possibly not being able to reach an age of fertility or carrying on a productive community as complex creatures with long gestation periods need a suitable environment to survive in during the pregnancy and then the young need to be raised to age of fertility.  Its a little more complicated then just bumping and grinding.  So you actually need to go further than the age of fertility especially if parenting is needed.  Whoops forgot about that huh? 

There are many cases in the animal world where members of a population look after each other's offspring. Especially in humans, where the survival of the population is directly the survival of the children. It's not the simple nuclear family in the animal kingdom (including humans), biological parents are not needed for parenting. Forgot about that huh?  ::)

Gunwounds:  No not really, as i said before ... as the organism gets more complex, parenting or even community structure is needed so i guess only bumping and grinding isnt sufficient.  Ooops did i just make you wrong? (Rhetorical question)

However, as we are not discussing solely human organisms, in the animal kingdom once an organism gets to the age of where instinct has been set and can live on its own, the parent abandons it (unlike humans where parenting is kept for a much longer period). Also, reproducing is done at a larger pace than humans, since offspring can number into the dozens or even hundreds at a time. So yes, "bumping and grinding" is quite sufficient, and the little parenting the organisms need can be done soon after.

Gunwounds:  Uh? What? Oh you were saying?  Anything that degrades or shortens life is negative IMO.

But it does not matter in terms of survival. It is not negative in respect to survival if it allows the organism to reproduce before it dies. Even better if it doesn't kill it at all, but if it can reproduce then the "defect" isn't that negative to the population as a whole in terms of survival. This isn't individualistic morality here where one defect is negative if the genes are not perfect (this can easily get into racism, hint hint).

I am referring to the human race (or any organism) in general.  Sure Sickle Cell anemia may help africans resist malaria... but what if the same sickle cell anemia causes the entire african population to die out 1,000 years later due to it combining with some other mutation defects to make it lethal at birth or cause sterility?  You have to look Big Picture in this situation when you are talking billions of years of compounding mutations... if the mutations are generally destructive and degrading (which due to probability they are) to the organism then it will increase the chances of the organism ending up extinct.

And due to probability a lot of populations have died because of these compounds. But the ones that have not are here as we see today. This is an odd topic of debate, since we can clearly see that organisms have lived for the past hundreds of millions of years, and even simple cellular organisms further than that. And since we know mutations occur, we can safely deduct that you are wrong. Aw, it's okay. Hug?

Imagine people who are lactose intolerant and their genes do not code for the enzyme that breaks down lactose sugar.  What if the negative mutations compounded and they obtained similar defects and ended up not being able to digest any sugars (frustose, glucose, sucrose) and ending up starving shortly after birth?  How is that mutation not negative?  How is that situational?  I'll stop asking rhetorical questions cause I hope by now you understand.

If that happened, the organisms born with that gene will die off and allow the populations without the gene to flourish further (especially with the increase in resources since the other population doesn't eat when it's dead). In the environments that allow this to happen, however. But this is only happening because the environment led to the steps of glucose being necessary for enzymatic functions, etc. If the environment was different from the start, life may have found a different way to live and thus the lack of digestion of sugars would not be negative. You see, it's relative. Genes have entirely different outcomes when faced with a different environment.

[Dante]

This thread has followed the pattern of its many predecessors and moved into offtopic vendetta. Granted the points may have significance in a related argument, but it would be nice if we could stick to viral (or possibly bacterial?) impact on the evolution of Eukaryotes.

Since the majority of my points weren't dealt with, I see no reason to wade back in until we return to the topic at hand.

[Dude_Doc]

Sure, I can just see the logic.

GOD: Yes, these people are going to need lots of methane to help them power things. I know! I'll create a whole lot of it for them and put it on a planetoid a few million miles away. Genius!

Pff. You might as well argue that plants exist for the use of vegetarians or that we wouldn't have summer without the sun. These are nonsensical statements based on the fact that some things exist in a pattern. 'Oo, cows eat grass. Grass must have been created for cows!'

Also, seasons are controlled by the slight tilting of the Earth on its axis. Moon has little to no effect on that. And the bacterium isn't newly discovered, the virus is.

I said it depends on how people look at it. You think that it is coincidence. This was my point.

[GUNWOUNDS]

But this is only happening because the environment led to the steps of glucose being necessary for enzymatic functions, etc. If the environment was different from the start, life may have found a different way to live and thus the lack of digestion of sugars would not be negative. You see, it's relative. Genes have entirely different outcomes when faced with a different environment.

Actually digesting sugars is due to us being carbon based life-forms... so ...uh... there could not have been another way... carbon is the only reasonable building-block for life and therefore we were gonna end up eating sugar no matter what.. Hate to burst your bubble buddy.  ;D

About your golfball scenario.... the problem is that in your example... the golfball WAS launched and we knew that due to gravity... IT HAD TO COME DOWN 100%.  So no its not surprise that a golf ball had to come down on a blade of grass.  But life did NOT have to exist... because scientists can create the "right conditions" in test tubes and in large contraptions.... but life doesnt happen.  Gee i guess there is something more than just having the right conditions.  So lets get this straight.  Random factors with the right conditions produced life successfully... but mankind trying to intelligently manipulate the situation ALONG with the right conditions CANNOT replicate life?  dubbya tee eff mate?  Give me enough ball swings and eventully i will hit the same blade of grass.... we have given scientists plenty of swings but they cannot replicate life.  I guesss more is required than just "the right condtions"  ;)

Guns