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Author Topic: How do viruses pack more information into the same sized genome?  (Read 20916 times)

Offline Asyncritus

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I was absolutely gobsmacked to read this:

"However, a few years ago a surprising discovery was made by a group of biochemists at Cambridge University. While working on the DNA of a small virus, they discovered that it contained more information than could be accounted for if the genes were arranged in a linear array of discrete sequences.

For some time this discrepancy was very puzzling and the explanation, when it came, astonished the biological world.

After the exact sequence of the DNA of the virus had been worked out, the discovery was made that in certain regions two genes were embedded together in the same sequence, that is to say, they overlapped.

When two genes overlap in the same sequence the information for both encoded proteins is contained in one DNA sequence in the same way as one sequence of symbols in morse code can contain information for 2 words and be read in 2 different ways.

M... A... N... A
_ _ . _ _ . . _ . . .
....... M . I . N.. I

[I've had to insert spacing dots between the letters to keep them in the right places relative to the code.]

Thus the discrepancy between the coding potential and the number of proteins synthesized was explained by a mechanism of wonderful ingenuity...."

"Another compacting device, which has been shown to be utilised in living systems and which again has no strict analogy in our own technology, is the use of breakdown products of proteins to perform all sorts of functions often quite unrelated to the original function of the 'mother protein.

Thus many protein functions are compacted into an original molecule.

The process begins by the synthesis of the original protein which, after performing its function, is broken down in the cell into two smaller proteins, each of which perform two further functions. These two new proteins are again broken down into still smaller proteins capable of yet further functions.

The device is somewhat analogous to having a whole tol kit compacted within the first tool we require to initiate a particular operation, and when the initial operation is complete. the tool breaks down into the next two tools required for the operation, and so on until the operation is complete."

There is no conceivable way that these devices could have a chance origin, and divine construction is really the only satisfactory explanation.
« Last Edit: 13/11/2008 21:11:58 by Asyncritus »


 

Offline BenV

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All very interesting, until the last line, where it fell apart into nonsense.  There can be no sensible debate between evolution and intelligent design.  You are trying to use a philosophy to tell us that science is wrong.  I don't subscribe to your philosophy.
 

Offline Evie

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Indeed, Ben.

Once again, this comes down simply to the fact that some of us feel it is perfectly reasonable that nature can produce such elegant mechanisms and others feel that there needs to be some sort of intelligent force behind it.

Either way, I think wonderful discoveries like this can allow persons of either persuasion to marvel at the beautiful and intricate world we live in, strengthening our faith or our respect for nature.
 

Offline RD

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I did ask Asyncritus in a previous thread to account for the appearance of new viruses, (SARS AIDS, H571, etc), without mutation/evolution.

He is now telling us that God creates viruses.
So God has designed divinely perfect cell replication machinery only to create perfect viral spanners to throw in the works.

Surely this is a contradiction in terms: if all cells were "carefully and competently designed" then none could be parasitized by virus,
if viruses were also "carefully and competently designed" then why aren't all cells hosts to virus ?.

The answer is genetic variation in cells and viruses caused by random mutations, i.e. evolution, not creation.

For the benefit of those other than Asyncritus: complexity is not proof of design.
« Last Edit: 13/11/2008 17:24:06 by RD »
 

Offline DoctorBeaver

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If this amazing bit of coding is so good, why didn't the creator use it everywhere?
 

Offline DoctorBeaver

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I did ask Asyncritus in a previous thread to account for the appearance of new viruses, (SARS AIDS, H571, etc), without mutation/evolution.

He is now telling us that God creates viruses. So God has created divinely perfect cell replication machinery only to create a perfect viral spanners to throw in the works.

Surely this is a contradiction in terms: if all cells were "carefully and competently designed" then none could be parasitized by virus, if viruses were also "carefully and competently designed" then why aren't all cells hosts to virus ?.

The answer is genetic variation in cells and viruses caused by random mutations, i.e. evolution, not creation.

For the benefit of those other than Asyncritus: complexity is not proof of design.


Maybe God is a virus and it only created everything else so his children could thrive.
 

Offline RD

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Either way,
I think wonderful discoveries like this can allow persons of either persuasion to marvel at the beautiful and intricate world we live in, strengthening our faith or our respect for nature.

This is not a "depends-on-the-way-you-look-at-it" issue: logically the "intelligent design" hypothesis is without foundation.

Bear in mind Evie that Asyncritus has asserted that viruses are designed by god, the inescapable implication being that viral disease is God's will. If this were the case vaccination would be attempting to thwart God's will, which is evil blasphemy which should be stopped.

Do you not think Asyncritus should be challenged on his groundless and pernicious assertion that viruses are made by God ?.

Scientists should not "back off" when confronted by those who promote this harmful "intelligent design" hypothesis: give them no quarter.
« Last Edit: 13/11/2008 18:50:18 by RD »
 

Offline Bored chemist

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The assertion "There is no conceivable way that these devices could have a chance origin,"
is simply, factually wrong, I can conceive of a way that such a thing could have a chance origin.

I only need to cite one counter example (me) to prove that Asyncritus's sugestion is false.

End of any sensible debate.
 

Offline Asyncritus

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I did ask Asyncritus in a previous thread to account for the appearance of new viruses, (SARS AIDS, H571, etc), without mutation/evolution.

I'm pretty sure you don't read my posts. I said in the other thread, that micro-evolution occurs. That some speciations have taken place. Did you read that, or were your blinding prejudices too powerful?

Mutations in viruses and bacteria are examples of such micro-evolution. When you can demonstrate mutations producing new families or orders better yet, then you'll have a leg to stand on.

Quote
He is now telling us that God creates viruses.
So God has designed divinely perfect cell replication machinery only to create perfect viral spanners to throw in the works.

I'm certain He does - because there is a thing called sin on the planet, which makes things subject to death and disease and disaster.

Otherwise we'd be a race of immortal sinners. The very thought is fearful. Just imagine Hitler and Hussain living forever!

Quote
Surely this is a contradiction in terms: if all cells were "carefully and competently designed" then none could be parasitized by virus,
if viruses were also "carefully and competently designed" then why aren't all cells hosts to virus ?.

The answer is genetic variation in cells and viruses caused by random mutations, i.e. evolution, not creation.

Sure, random mutations cause variation.
Nobody is denying that. DID YOU READ THAT? OR MISSED IT AGAIN?

But
a. mutations are either neutral, or harmful and

b.The number of beneficial mutations is infinitesimal and don't really count.

So they do not produce new, better organisms, but are merely retrograde steps. So how did 14 new phyla arise in the Cambrian?

Try answering that question without having another fit, willya?

Quote
For the benefit of those other than Asyncritus: complexity is not proof of design.

I never said complexity BY ITSELF is proof of design.

There are 3 things which must be present before we can validly say 'design is present'.

1 Complexity

2 Specificity

3 Contingency.

Each is present in the virus example above.

1 It is an exceedingly complex phenomenon

2 It's purpose is specifically to save space on the genome

3 Contingency means it couldn't 'just happen'. This definitely didn't just happen.

 
 

Offline DoctorBeaver

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I'm pretty sure you don't read my posts. I said in the other thread, that micro-evolution occurs. That some speciations have taken place. Did you read that, or were your blinding prejudices too powerful?

Mutations in viruses and bacteria are examples of such micro-evolution. When you can demonstrate mutations producing new families or orders better yet, then you'll have a leg to stand on.

So the creator's designs were improved upon?
 

Offline Asyncritus

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This is not a "depends-on-the-way-you-look-at-it" issue: logically the "intelligent design" hypothesis is without foundation.

Quote
Bear in mind Evie that Asyncritus has asserted that viruses are designed by god, the inescapable implication being that viral disease is God's will. If this were the case vaccination would be attempting to thwart God's will, which is evil blasphemy which should be stopped.

Do you not think Asyncritus should be challenged on his groundless and pernicious assertion that viruses are made by God ?.

Please do challenge. But do so constructively please.

As I mentioned in my previous post, before we can say that design is present, then 3 things have to be present.

There are 3 things which must be present before we can validly say 'design is present'.

1 Complexity

2 Specificity

3 Contingency.

Each is present in the virus example above.

1 It is an exceedingly complex phenomenon

2 It's purpose is specifically to save space on the genome

3 Contingency means it couldn't 'just happen'. This definitely didn't just happen.

Now would you care to refute those 3 requirements and the worked example?
Quote
Scientists should not "back off" when confronted by those who promote this harmful "intelligent design" hypothesis: give them no quarter.

I fully agree with you on this. But do argue constructively and logically. In the same way as you view ID as harmful and pernicious, I view evolution as dangerous and demeaning to the human intellectual powers.

Now we've got the name calling out of the way, would you care to engage in some rational debate, and not disappear off the scene?

May I suggest 'The Origin of Instinct' as a good place to start?

I propose that instinct is of divine origin.

Fancy a go, in the name of logic and rationality,and for the benefit of the interested, non-writing, non-shouting readers of the board?
 

Offline Asyncritus

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I'm pretty sure you don't read my posts. I said in the other thread, that micro-evolution occurs. That some speciations have taken place. Did you read that, or were your blinding prejudices too powerful?

Mutations in viruses and bacteria are examples of such micro-evolution. When you can demonstrate mutations producing new families or orders better yet, then you'll have a leg to stand on.

So the creator's designs were improved upon?

No - they were varied.

He created things with a built in capacity to vary. Just look around you.

But there are very definite limits as to how much variation can occur. There is a Law of Reversion to the Mean as Luther Burbank called it. Things can vary just so much, and no further. Burbank depended on plant breeding for his living, and wasn't one of these cross-eyed evolutionists in an ivory tower somewhere, far removed from the real world.

“There is a law of which I have not yet spoken that is useful to plant-breeders, as well as being a limitation on them. It is called the ‘law of the Reversion to the Average.’

I know from my experience that I can develop a plum half an inch long or one two and a half inches long, with every possible length in between, but I am willing to admit that it is hopeless to try to get a plum the size of a small pea, or one as big as a grape-fruit. I have daisies on my farms little larger than my finger nail and some that measure six inches across, but I have none as big as a sunflower, and never expect to have….. In short, there are limits to the developments possible, and these limits follow a law” (BURBANK 1939).
 

Offline Asyncritus

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If this amazing bit of coding is so good, why didn't the creator use it everywhere?

He probably had enough space in the larger genomes.

BTW who keeps changing my topic titles?
 

Offline DoctorBeaver

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There are 3 things which must be present before we can validly say 'design is present'.

1 Complexity

2 Specificity

3 Contingency.

Can you explain your reasoning as to why those 3 criteria indicate design exclusively and cannot be the result of evolution?
 

Offline DoctorBeaver

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Your topic title was changed as questions are better for search engines to find.
 

Offline DoctorBeaver

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No - they were varied.

He created things with a built in capacity to vary. Just look around you.

Yes, look around you. Almost everything you see can be explained scientifically.

My big problem with adherents of ID is that they come out with trite statements such as you have; "It can't be anything but...", "Scientists were surprised to find...", etc. The 1st of those statements is never backed up by any kind of proof that it can't be anything but intelligently designed. The eye is a case in point. It is claimed by IDers that there has not been enough time for the eye to have evolved. Well, sorry, but to me the fact that it is there and that evolution has been seen to be correct (or, at least, the mechanism of evolution), is proof that there indeed has been time for the eye to evolve.

Scientists are indeed surprised at times by what they find. A case in point was the discovery of, I believe, the Muon. One of the scientists on the team who discovered it exclaimed "Who ordered that?". But the Muon was investigated and is now a part of the Standard Model.

Throughout its history science has been full of "I didn't expect that" moments. But it is not automatically assumed that because we cannot explain something immediately that it must be the work of a Creator. Nor do I take the view that "There are some things we are not meant to know". That is total rubbish. There are indeed  things that we will probably never know - was there anything before the Big Bang? is ours the only universe? - but there are physical reasons why we will never know such things; no kind of Creator has said "Whoah, that's far enough" and put things beyond our reach deliberately.
« Last Edit: 13/11/2008 21:52:35 by DoctorBeaver »
 

Offline RD

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I did ask Asyncritus in a previous thread to account for the appearance of new viruses, (SARS AIDS, H571, etc), without mutation/evolution.

I'm pretty sure you don't read my posts. I said in the other thread, that micro-evolution occurs. That some speciations have taken place. Did you read that, or were your blinding prejudices too powerful?

Mutations in viruses and bacteria are examples of such micro-evolution. When you can demonstrate mutations producing new families or orders better yet, then you'll have a leg to stand on.

Quote
He is now telling us that God creates viruses.
So God has designed divinely perfect cell replication machinery only to create perfect viral spanners to throw in the works.

I'm certain He does - because there is a thing called sin on the planet, which makes things subject to death and disease and disaster.

Otherwise we'd be a race of immortal sinners. The very thought is fearful. Just imagine Hitler and Hussain living forever!

Quote
Surely this is a contradiction in terms: if all cells were "carefully and competently designed" then none could be parasitized by virus,
if viruses were also "carefully and competently designed" then why aren't all cells hosts to virus ?.

The answer is genetic variation in cells and viruses caused by random mutations, i.e. evolution, not creation.

Sure, random mutations cause variation
. Nobody is denying that. DID YOU READ THAT? OR MISSED IT AGAIN?

But
a. mutations are either neutral, or harmful and

b.The number of beneficial mutations is infinitesimal and don't really count.

So they do not produce new, better organisms, but are merely retrograde steps. So how did 14 new phyla arise in the Cambrian?

Try answering that question without having another fit, willya?

In the above post you state that evolution does occur via rare beneficial genetic mutations, i.e. you are an evolutionist.
Environmental pressures acting upon genetic variations caused by random mutation, (which you have acknowledged occur), are sufficient to explain the diversity of life on Earth, no creator required.
You simply wish there to be such an entity to support your unjustifiable opinions, e.g. that viral disease is divine punishment for those whom you judge to be "sinners". BTW if viruses did not exist humans (& other animals) would not be "immortal", however there would be considerably less childhood mortality. Perhaps Asyncritus can tell us what sin an infant/child could have committed which justifies a death sentence via viral illness.

PS
    are animals who suffer from / die from viral disease also "sinners" ?, what sort of sin must a bird commit to get H5N1 ?.
     (I suppose a talking parrot could blaspheme).
« Last Edit: 15/11/2008 19:11:32 by RD »
 

Offline Bored chemist

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".The number of beneficial mutations is infinitesimal and don't really count.
"
Not evinced annd probably not true.
Why the need keep making false statements in support of some all powerfull god?
 

Offline Don_1

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For pity's sake Asyncritus, sing a different song!
 

Offline Asyncritus

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There are 3 things which must be present before we can validly say 'design is present'.

1 Complexity

2 Specificity

3 Contingency.

Can you explain your reasoning as to why those 3 criteria indicate design exclusively and cannot be the result of evolution?

There's a whole book on the subject called Intelligent Design by William Dembski. He holds, I think, 3 PhDs in Maths, Philosophy and Theology.

It's far too much to attempt to reproduce the arguments here, but even at an intuitive level you can see that that is really the case.

There are complex things which are not designed, and may create the appearance of design, so by itself thais is not enough.

Contingency means that something couldn't just happen by itself - meaning that there is input of constructive information which is not available without thought. As a good example, the viral DNA could not code for 1 protein without a huge amount of information being present - mRNA, transcriptases, ribosomes,  translators etc etc.

To find it coding for TWO proteins using the SAME DNA space for the sake of economy, requires extremely high level information input. That is what I mean by 'contingency'.

Specificity is intuitively obvious. A tool or something else is specifically designed to do a particular job, and very often requires accurate measurements and other strict design detailing.

By itself, any one of the three COULD have 'just happened.' But put the 3 together and the statistical improbability is incalculable.

As I say, in so many cases in the natural world, these 3 features are clearly present. The eye, somebody mentioned is the classic case in point: but greater by very far, is the brain, and greater still is instinct.
 

Offline Asyncritus

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".The number of beneficial mutations is infinitesimal and don't really count.
"
Not evinced annd probably not true.
Why the need keep making false statements in support of some all powerfull god?

Go find me a dozen examples of mutations producing new species. There's the whole internet out there for you to search.

Or are you bored to try?
 

Offline DoctorBeaver

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I'll give you 13 without even breaking sweat - Galapagos finches.
 

Offline BenV

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But do argue constructively and logically.
I think this is where people have a problem with you - you insist that we argue constructively and logically whilst holding on the the illogical fallacy that there is a god.  By choosing to blur the lines between religious philosophy and science you reject any and all logic that we can present to you.  This means that all arguments with you are pointless.

You also seem to be unaware that genetic translations, substitutions and deletions play a role in addition to mutations, so any probability you have worked out based on mutation rate alone is irrelevant.
 

Offline SquarishTriangle

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If god is so concerned about making things incredibly efficient, why are you antagonising his efforts by making redundant arguments on a website where the people are clearly in no rush to be persuaded by you? He would be ashamed.
 

Offline _Stefan_

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He's hoping to brainwash some innocent readers who are looking for real answers.

Isn't there some effective method of silencing forum trolls?
 

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