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Author Topic:   Is there any proof of beneficial mutations?
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 76 of 166 (580151)
09-07-2010 10:46 PM
Reply to: Message 74 by ICANT
09-07-2010 10:36 PM


Re: Cause of mutation?
How do you know the trait was acquired rather than lost?
I told you, already. If the trait had been present in the founder individual than all colonies would have survived; any particular mutation is highly unlikely so only a small - not even noticeable - number of bacteria would have lost the trait and been killed by the antibiotic.
Replica plating would have produced replicas of all colonies. It only takes a single individual to form a colony, and at least one - though mathematically it's more like almost all the individuals - would not have lost the trait.
That's not what was observed. Many colonies did not replicate at all. Any particular mutation is highly unlikely and if a colony doesn't replicate it's because of the millions of bacteria in a discreet colony, not a single one was fit to survive on the test media.
The source of almost every trait in a bacteria is vertical gene transfer - direct inheritance from its parent. If a trait is widespread throughout a population it primarily got there by direct inheritance. Because antibiotic resistance was not initially widespread we know that it was the acquired trait, rather than the reverse as you propose. Because the bacteria were clonal and the species is haploid we know the source was mutation. And we know that mutation is random.

This message is a reply to:
 Message 74 by ICANT, posted 09-07-2010 10:36 PM ICANT has replied

Replies to this message:
 Message 77 by ICANT, posted 09-07-2010 11:31 PM crashfrog has replied

  
ICANT
Member
Posts: 6769
From: SSC
Joined: 03-12-2007
Member Rating: 1.5


Message 77 of 166 (580156)
09-07-2010 11:31 PM
Reply to: Message 76 by crashfrog
09-07-2010 10:46 PM


Re: Cause of mutation?
Hi crash,
crashfrog writes:
I told you, already. If the trait had been present in the founder individual than all colonies would have survived; any particular mutation is highly unlikely so only a small - not even noticeable - number of bacteria would have lost the trait and been killed by the antibiotic.
Half of the colonies could not have lost their immunity.
But half of the colonies could have mutated to the point they were immune.
That does not compute.
crashfrog writes:
Because antibiotic resistance was not initially widespread we know that it was the acquired trait, rather than the reverse as you propose. Because the bacteria were clonal and the species is haploid we know the source was mutation. And we know that mutation is random.
That is a contradictatory statement.
"Because antibotic resistance was not initially widespread."
So it did exist just everybody did not have resistance.
Then you follow with, "we know that it was the acquired trait".
So you are saying it was an acquired trait because everybody initally did not have the trait.
That don't compute either.
What does compute is that some bacteria received the trait from their parents and others did not receive the trait for some reason and they died.
Now your statement, "was not initially widespread" proves my point thanks.
The information was in the DNA.
God Bless,
Here you admit antibotic restance existed.

"John 5:39 (KJS) Search the scriptures; for in them ye think ye have eternal life: and they are they which testify of me."

This message is a reply to:
 Message 76 by crashfrog, posted 09-07-2010 10:46 PM crashfrog has replied

Replies to this message:
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DrJones*
Member
Posts: 2284
From: Edmonton, Alberta, Canada
Joined: 08-19-2004
Member Rating: 6.8


Message 78 of 166 (580157)
09-07-2010 11:41 PM
Reply to: Message 77 by ICANT
09-07-2010 11:31 PM


Re: Cause of mutation?
What does compute is that some bacteria received the trait from their parents and others did not receive the trait for some reason and they died.
There are no "parents". Bacteria reproduce asexually, all the bacteria in the colony are clones of the original, plus whatever errors/mutations might have occurred in the DNA copying process. If the initial bacteria has no resistance to the anti-biotic and some of the following generations do, the only way they could have gained that resistance is by mutation.

It's not enough to bash in heads, you've got to bash in minds
soon I discovered that this rock thing was true
Jerry Lee Lewis was the devil
Jesus was an architect previous to his career as a prophet
All of a sudden i found myself in love with the world
And so there was only one thing I could do
Was ding a ding dang my dang along ling long - Jesus Built my Hotrod Ministry

Live every week like it's Shark Week! - Tracey Jordan
Just a monkey in a long line of kings. - Matthew Good
If "elitist" just means "not the dumbest motherfucker in the room", I'll be an elitist! - Get Your War On
*not an actual doctor

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crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 79 of 166 (580161)
09-07-2010 11:56 PM
Reply to: Message 77 by ICANT
09-07-2010 11:31 PM


Re: Cause of mutation?
Half of the colonies could not have lost their immunity.
A colony is millions, perhaps hundreds of millions of individual bacteria - so many, in such a large pile, that they can be seen by the naked eye.
It only takes one viable individual to form a colony. It only takes one. If you replica plate a colony, and no colony forms on the replica plate, then that means not a single one of those millions of individuals was fit to survive on the replica medium.
So, no, half of the colonies could not have lost their resistance - that would mean that hundreds of millions of individual bacteria all coincidentally had the same unlikely mutation. Odds that border on absurdity.
But half of the colonies could have mutated to the point they were immune.
Just one individual in the colony needs to have the mutation, get transferred as part of the replica process, and thrive on the replica medium to form a replicated colony there. It only takes one. One specific mutation in one individual out of hundreds of millions of individuals, all mutating? Those are very good odds. The odds that you will win the lottery are very small. The odds that someone will win the lottery usually approach certainty (if enough people buy tickets.)
That does not compute.
Do you need me to walk you through the concept of "replica plating"? It's not difficult, I promise, and it might resolve your confusion, here.
So it did exist just everybody did not have resistance.
Right. It had to exist in the population among isolated individuals or else none of the colonies would replicate. But it could not have been widespread or else all of the colonies would replicate.
What does compute is that some bacteria received the trait from their parents and others did not receive the trait for some reason and they died.
A bacterium has only one parent, they reproduce by fission (not by sexual intercourse) and the "child" of a bacteria (traditionally called a "daughter") receives the full compliment of its mother's genetics. That's not true of diploid species like humans or pea plants (which obey Mendel's laws) but it is true of bacteria. They have a single parent, all of whose genes they inherit.
If a large number of bacteria had possessed the trait and some number of them had lost it, every colony would have replicated. If half of the bacteria had possessed the trait and half had lost it, every colony would have replicated. If .001% of the bacteria had possessed the trait and 99.999% of the bacteria had lost it, every colony would have replicated. It only takes a single viable individual to form a colony.
Every colony did not replicate. Only a few (half?) of them did. That proves that antibiotic resistance was such a rare trait amongst the entire plate of bacteria that it could only have arisen by random mutation.
The information was in the DNA.
As a result of random mutation. The proof of this is that some colonies replicated and some did not, which I've explained.
Here you admit antibotic restance existed.
Well, obviously. After all bacteria were transferred to growth media with antibiotic in it, and they survived and thrived there anyway. Obviously they had resistance before they were transferred; if not, they all would have died.
The resistance emerged as a result of random mutation. The proof of this is that not every colony replicated - some colonies did not have a single individual out of millions or even hundreds of millions with antibiotic resistance. That's proof that the trait was far too rare to be the result of inheritance; proof that the trait emerged by random mutation.

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 Message 77 by ICANT, posted 09-07-2010 11:31 PM ICANT has replied

Replies to this message:
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ICANT
Member
Posts: 6769
From: SSC
Joined: 03-12-2007
Member Rating: 1.5


Message 80 of 166 (580168)
09-08-2010 12:32 AM
Reply to: Message 79 by crashfrog
09-07-2010 11:56 PM


Re: Cause of mutation?
Message 10 Moved to
Edited by ICANT, : Moved message

"John 5:39 (KJS) Search the scriptures; for in them ye think ye have eternal life: and they are they which testify of me."

This message is a reply to:
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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 81 of 166 (580179)
09-08-2010 1:41 AM
Reply to: Message 69 by ICANT
09-07-2010 8:42 PM


Rubbing Salt in Wound
Penicillin was first used in 1871 but was not mass produced until just before the invasion of Normandy. It was great for colds in the 50's.
Really? Did you ever have a course of penicillin cure a cold?
Do you know of anyone on the planet who had their cold cured by penicillin?
I was there too ICANT. In the 50's penicillin was lousy on colds. To this day it's still lousy on colds. So are amoxicillin, oxacillin, methecillin and all the other derivatives of penicillin produced anywhere ever.
Even in the 50's, ICANT, doctors know better than to prescribe penicillin for a cold.
Do you know why?

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dennis780
Member (Idle past 4776 days)
Posts: 288
From: Alberta
Joined: 05-11-2010


Message 82 of 166 (580196)
09-08-2010 6:56 AM
Reply to: Message 65 by Huntard
09-07-2010 8:29 AM


Re: Cause of mutation?
Which is not random.

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dennis780
Member (Idle past 4776 days)
Posts: 288
From: Alberta
Joined: 05-11-2010


Message 83 of 166 (580197)
09-08-2010 6:57 AM
Reply to: Message 66 by greyseal
09-07-2010 11:04 AM


Re: Cause of mutation?
quote:
but if you ascribe conscious thought or even specifically directed mutation for the results you mention, then everything in your post is wrong.
My points are directed to a form of instinctive behaviour, rather than conscious thought persay.

This message is a reply to:
 Message 66 by greyseal, posted 09-07-2010 11:04 AM greyseal has replied

Replies to this message:
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dennis780
Member (Idle past 4776 days)
Posts: 288
From: Alberta
Joined: 05-11-2010


Message 84 of 166 (580198)
09-08-2010 7:04 AM
Reply to: Message 67 by crashfrog
09-07-2010 12:03 PM


Re: Cause of mutation?
quote:
Bacteria mutate all the time. Constantly.
Though this is true, it is also not my point. My point was, and is, that bacteria have the ability to respond to different conditions not by random chance, but by understanding conditions:
quote:
Aerobic bacteria avoid the twin dangers of too little oxygen or too much oxygen by utilizing their electron transport system as the sensor for a positive behavioral response to oxygen (aerotaxis) and a different receptor for negative aerotaxis.
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=...
quote:
It's literally the result of chance that any bacteria are initially resistant to an antibiotic when it's added.
Again, though this may be true, many bacteria have the built in capacity to respond to their environment without mutational change, or have built in genetic ability to respond to their environment causing mutational change.
quote:
They don't affect bacteria as a whole; otherwise every bacteria would instantly mutate as soon as the antibiotic was added.
This would entirely depend on the bacteria, since different defence mechanisms are have better responses than others.

This message is a reply to:
 Message 67 by crashfrog, posted 09-07-2010 12:03 PM crashfrog has replied

Replies to this message:
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dennis780
Member (Idle past 4776 days)
Posts: 288
From: Alberta
Joined: 05-11-2010


Message 85 of 166 (580209)
09-08-2010 7:44 AM
Reply to: Message 68 by Taq
09-07-2010 12:50 PM


Re: Cause of mutation?
quote:
they demonstrated that these mutations occurred in the absence of antibiotics.
Firstly, I can't open the file, because it is Adobe. I am using a work computer, and it's locked, so I can't download it either...can you copy and paste just this particular info, or private message it to me?
quote:
I would describe it more as bacteria acting like automatons . . . like robots.
I agree, I used the word instinctive earlier, but your word choice is much better. It is more than likely an uncontrollable response, but the response is beneficial. However, the particular point I am trying to make is that bacteria do have the ability to adapt to their environment without any mutational change.
quote:
Would you consider giving children deadly and painful diseases an "intelligent" decision?
Whoa, this is a topic changer. I'll respond.
First, I have no idea what God's plan is, only what is taught in the Bible. I cannot speak to God's mindset or reasoning for anything, only that, if I am correct, everything that happens he has planned (again, only if I am correct).
Second, natural genetic breakdown over time occurs because of sexual reproduction (minus an individuals mutations within their life). If (AND again, only if I am correct) Adam and Eve had not eaten from the forbidden tree, they would not have reproduced, and lived forever. Although I am sure this is a topic for another thread, genetic breakdown from sexual reproduction would have been eliminated.
But that just brought an interesting question to my head...if Adam and Eve did not eat from the tree and lived forever, would their dna have mutated eventually to the point where they would die?
I should start a thread...

This message is a reply to:
 Message 68 by Taq, posted 09-07-2010 12:50 PM Taq has replied

Replies to this message:
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crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 86 of 166 (580243)
09-08-2010 10:13 AM
Reply to: Message 84 by dennis780
09-08-2010 7:04 AM


Re: Cause of mutation?
My point was, and is, that bacteria have the ability to respond to different conditions not by random chance, but by understanding conditions:
Yes, for instance the lac operon, which upregulates production of beta-galactosidase for the metabolism of lactose in the presence of lactose and the absence of glucose. If lactose is not present beta-Gal is not produced. If glucose is not absent beta-Gal is not produced. Obviously organisms have an innate, preprogrammed capacity to respond to their environment; in the case of bacteria this usually takes the form of changes in levels of protein expression.
But the origin of the lac operon is the same as the origin of all genes - random mutation and natural selection. And if bacteria had the innate genetic ability to resist antibiotics already encoded in their genes all bacteria would be resistant to antibiotics.
That's not what we observe at all. When we introduce an antibiotic to a culture of bacteria the first thing that happens is that almost all of them die. Where was their "non-mutational adaptability"? Where was their "innate genetic resistance"?
Nowhere to be found, because it was not there. When you add an antibiotic to culture the population crashes, drops to a handful of individuals - the ones who had mutated into a resistant strain - and then the population rebounds as the resistant individuals exploit the sudden lack of competition for medium and grow exponentially.
Random mutation is the only explanation for that pattern. If bacteria had a pre-programmed innate resistance to antibiotics the antibiotics wouldn't work. They wouldn't ever work. You could at most expect to kill the 10% or so of bacteria, the ones who had lost their resistance by harmful mutation, and that's essentially pissing in the ocean. I don't think you're entirely grasping the notion of "exponential growth." An antibiotic has to kill almost every single bacterium to be an effective medical treatment.
This would entirely depend on the bacteria, since different defence mechanisms are have better responses than others.
Bacterial colonies are clonal. If they have different "defense mechanisms" then the only explanation for that is random mutation of their defense mechanisms.

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crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 87 of 166 (580245)
09-08-2010 10:15 AM
Reply to: Message 82 by dennis780
09-08-2010 6:56 AM


Re: Cause of mutation?
Selection is never random, but mutation always is. By fairly simple laws of chemistry it has to be; mutagens are necessarily going to attack DNA at random locations simply due to Brownian motion.

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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(1)
Message 88 of 166 (580261)
09-08-2010 11:32 AM
Reply to: Message 85 by dennis780
09-08-2010 7:44 AM


Re: Cause of mutation?
Firstly, I can't open the file, because it is Adobe. I am using a work computer, and it's locked, so I can't download it either...can you copy and paste just this particular info, or private message it to me?
The technique is explained here:
Plate replica technique
You start this experiment with a single bacterium that forms a single colony on an agar plate. You then transfer that single colony to some liquid media to make more bacteria. At a certain point you spread this liquid media over an agar plate and let it grow overnight producing a lawn of bacteria. All of this is done on plates that do not contain antibiotic.
Using a stamp-like apparatus you then transfer bacteria from the master plate (the plate with the lawn of bacteria) to several plates containing bacteria. What you find is that resistant colonies grow on the plate, and they occur at the same spot on each plate. This is because they originate from bacteria on the same spot on the master plate. Therefore, there are resistant bacteria on the master plate that have never been exposed to antibiotic, and those resistant clones arose through mutation from the original bacterium since that original bacterium was not resistant (as evidenced by the non-resistant phenotype of the vast majority of bacteria). As the Lederberg's put it, they were pre-adapted and that adaptation occured in the absence of antibiotics.
However, the particular point I am trying to make is that bacteria do have the ability to adapt to their environment without any mutational change.
And at the same time, some adapation requires mutations in the DNA.
First, I have no idea what God's plan is, only what is taught in the Bible. I cannot speak to God's mindset or reasoning for anything, only that, if I am correct, everything that happens he has planned (again, only if I am correct).
So it may be part of God's plan to give children horrific genetic diseases that kills them before they ever reach adulthood? Yikes.
Second, natural genetic breakdown over time occurs because of sexual reproduction (minus an individuals mutations within their life).
The mechanisms that produce beneficial and detrimental mutations are the same. You can't call it "genetic breakdown" when it does something bad and "intelligent design" when it does something good. It is the same mechanism in both instances.
But that just brought an interesting question to my head...if Adam and Eve did not eat from the tree and lived forever, would their dna have mutated eventually to the point where they would die?
If Santa Claus did not have flying reindeer would he be able to deliver presents to all the children across the world?

This message is a reply to:
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Replies to this message:
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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 89 of 166 (580263)
09-08-2010 11:39 AM
Reply to: Message 77 by ICANT
09-07-2010 11:31 PM


Re: Cause of mutation?
Half of the colonies could not have lost their immunity.
Your numbers are way off. The Lederbergs reported that resistant clones occured in one in every 10 billion bacteria, and in in every 10 million for bacteriophage resistance.
Source: http://profiles.nlm.nih.gov/BB/A/B/F/J/_/bbabfj.pdf
So you are saying it was an acquired trait because everybody initally did not have the trait.
If it was present in the single bacterium that was the founder of the entire population then nearly the entire population (more than 99.999%) would be resistant. They weren't. Only one in 10 billion were antibiotic resistant after the culture had increased in number over time.

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greyseal
Member (Idle past 3861 days)
Posts: 464
Joined: 08-11-2009


Message 90 of 166 (580266)
09-08-2010 11:55 AM
Reply to: Message 83 by dennis780
09-08-2010 6:57 AM


Re: Cause of mutation?
dennis780 writes:
quote:
but if you ascribe conscious thought or even specifically directed mutation for the results you mention, then everything in your post is wrong.
My points are directed to a form of instinctive behaviour, rather than conscious thought persay.
if your are suggesting that "instinctive behaviour" can change genetic code deliberately to produce a specific outcome, then you are still wrong.
That's not evolution, that's lamarckianism. As a theory it predates evolution by some score of years and has been proven wrong more than a hundred years ago.
It recently saw some light because - and I'm sure I will be corrected here as this is off the top of my own head and I might be very wrong - there are some life-forms that can have different physical characteristics to their parents due to specific environmental factors...but that's due entirely to the "code" being in the genome already.
However, it's still not design and it's still not lamarckian vindication, it's an adaptation like any other that came about through chance and mutation.
Having a specific ability that impacts a limited and specific set of specific characteristics in the (unborn) offspring of a specific creature is not the same as having the ability to manipulate the genetic code deliberately to produce a certain outcome.

This message is a reply to:
 Message 83 by dennis780, posted 09-08-2010 6:57 AM dennis780 has replied

Replies to this message:
 Message 93 by dennis780, posted 09-10-2010 12:03 AM greyseal has replied

  
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