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Random mutations and adaptive mutations

Iredia
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4/10/2014 1:46:30 AM
Posted: 2 years ago
It is repeated that the way organisms evolve and speciate is through principal evolutionary mechanisms of random mutations and natural selection. However, in Wikipedia's article on directed mutations it is mentioned that the likes of Cairns advocated for the mutations which occurred when an organism was exposed to certain stresses. Despite, the amount of experimental evidence behind mechanisms in the cell and gene eg mobile genetic elements which are activated when an organism is exposed go certain environments, why are directed/adaptive mutations still overlooked in favor of ranfom mutations ?
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iamanatheistandthisiswhy
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4/10/2014 3:18:57 AM
Posted: 2 years ago
At 4/10/2014 1:46:30 AM, Iredia wrote:
It is repeated that the way organisms evolve and speciate is through principal evolutionary mechanisms of random mutations and natural selection. However, in Wikipedia's article on directed mutations it is mentioned that the likes of Cairns advocated for the mutations which occurred when an organism was exposed to certain stresses. Despite, the amount of experimental evidence behind mechanisms in the cell and gene eg mobile genetic elements which are activated when an organism is exposed go certain environments, why are directed/adaptive mutations still overlooked in favor of ranfom mutations ?

Is Cairns not referring to stress causing mutations that can be random anyway? It is a directed mutation in so much that it may affect a specific sight (area) on the gene, however it is still random. I hope this helps.

If I had a little more information to exactly what you were referencing maybe I could be more help.
Iredia
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4/10/2014 8:18:14 AM
Posted: 2 years ago
At 4/10/2014 3:18:57 AM, iamanatheistandthisiswhy wrote:
At 4/10/2014 1:46:30 AM, Iredia wrote:
It is repeated that the way organisms evolve and speciate is through principal evolutionary mechanisms of random mutations and natural selection. However, in Wikipedia's article on directed mutations it is mentioned that the likes of Cairns advocated for the mutations which occurred when an organism was exposed to certain stresses. Despite, the amount of experimental evidence behind mechanisms in the cell and gene eg mobile genetic elements which are activated when an organism is exposed go certain environments, why are directed/adaptive mutations still overlooked in favor of ranfom mutations ?

Is Cairns not referring to stress causing mutations that can be random anyway? It is a directed mutation in so much that it may affect a specific sight (area) on the gene, however it is still random. I hope this helps.

If I had a little more information to exactly what you were referencing maybe I could be more help.

Read Wikipedia's article on 'adaptive mutations'. Also read James Shapiro's huffpost blog (http:/m.huffpost.com/us/author/james-a-shapiro) for better context.
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iamanatheistandthisiswhy
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4/10/2014 8:57:04 AM
Posted: 2 years ago
At 4/10/2014 8:18:14 AM, Iredia wrote:
At 4/10/2014 3:18:57 AM, iamanatheistandthisiswhy wrote:
At 4/10/2014 1:46:30 AM, Iredia wrote:
It is repeated that the way organisms evolve and speciate is through principal evolutionary mechanisms of random mutations and natural selection. However, in Wikipedia's article on directed mutations it is mentioned that the likes of Cairns advocated for the mutations which occurred when an organism was exposed to certain stresses. Despite, the amount of experimental evidence behind mechanisms in the cell and gene eg mobile genetic elements which are activated when an organism is exposed go certain environments, why are directed/adaptive mutations still overlooked in favor of ranfom mutations ?

Is Cairns not referring to stress causing mutations that can be random anyway? It is a directed mutation in so much that it may affect a specific sight (area) on the gene, however it is still random. I hope this helps.

If I had a little more information to exactly what you were referencing maybe I could be more help.

Read Wikipedia's article on 'adaptive mutations'. Also read James Shapiro's huffpost blog (http:/m.huffpost.com/us/author/james-a-shapiro) for better context.

Okay, I think I get the question now. The answer is no, it is random.

If you have a set of 100 bugs say. If you then expose these bugs to a poison then say 98 of them die. the remaining 2 had a mutation that occurred on the same gene which prevented their death. This does not mean the mutation happened at the gene because it was directed. It just happens that random mutation is the mutation that provides resistance to the poison. If it was directed then all 100 bugs would survive as the poison would make all the bugs mutate at the same place on the same gene.

Hope that helps.
slo1
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4/11/2014 11:49:53 AM
Posted: 2 years ago
At 4/10/2014 1:46:30 AM, Iredia wrote:
It is repeated that the way organisms evolve and speciate is through principal evolutionary mechanisms of random mutations and natural selection. However, in Wikipedia's article on directed mutations it is mentioned that the likes of Cairns advocated for the mutations which occurred when an organism was exposed to certain stresses. Despite, the amount of experimental evidence behind mechanisms in the cell and gene eg mobile genetic elements which are activated when an organism is exposed go certain environments, why are directed/adaptive mutations still overlooked in favor of ranfom mutations ?

I would not call it overlooked. We are really only just starting to understand gene expression what it is dependent upon, when is it triggered, how many copies of genes impact it, what can go wrong with RNA, how "junk" dna may impact it, how methylation impacts it. It plays a very important role in evolution, especially in the health and overall wellness of the organism.

On the other hand if the code is not in the sequence to do XYZ there is nothing but a random mutation that will change the code to to XYZ. I guess there is a theist viewpoint where a higher power may change the code to do XYZ.

The other way to think of it, is that the code is only the code. It is meaningless unless something is done with it. The "something" is all the factors that are involved with making protein/enzymes or disrupting the making of protein/enzymes.

There is no environmental factor that would cause me to grow a third arm on my butt and pass it to my children unless it changed my code or appended to the code via methylation to grow a third arm.

Like that "butt" bit?
Iredia
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4/11/2014 3:33:05 PM
Posted: 2 years ago
At 4/10/2014 8:57:04 AM, iamanatheistandthisiswhy wrote:
At 4/10/2014 8:18:14 AM, Iredia wrote:
At 4/10/2014 3:18:57 AM, iamanatheistandthisiswhy wrote:
At 4/10/2014 1:46:30 AM, Iredia wrote:
It is repeated that the way organisms evolve and speciate is through principal evolutionary mechanisms of random mutations and natural selection. However, in Wikipedia's article on directed mutations it is mentioned that the likes of Cairns advocated for the mutations which occurred when an organism was exposed to certain stresses. Despite, the amount of experimental evidence behind mechanisms in the cell and gene eg mobile genetic elements which are activated when an organism is exposed go certain environments, why are directed/adaptive mutations still overlooked in favor of ranfom mutations ?

Is Cairns not referring to stress causing mutations that can be random anyway? It is a directed mutation in so much that it may affect a specific sight (area) on the gene, however it is still random. I hope this helps.

If I had a little more information to exactly what you were referencing maybe I could be more help.

Read Wikipedia's article on 'adaptive mutations'. Also read James Shapiro's huffpost blog (http:/m.huffpost.com/us/author/james-a-shapiro) for better context.

Okay, I think I get the question now. The answer is no, it is random.

If you have a set of 100 bugs say. If you then expose these bugs to a poison then say 98 of them die. the remaining 2 had a mutation that occurred on the same gene which prevented their death. This does not mean the mutation happened at the gene because it was directed. It just happens that random mutation is the mutation that provides resistance to the poison. If it was directed then all 100 bugs would survive as the poison would make all the bugs mutate at the same place on the same gene.

Hope that helps.

I'm sure you didn't read Shapiro's blog. You should know that cell signalling (to help a cell respond to its environment) is part of what is responsible for directing the mutations that enable the survival of the two bugs in your scenario. This is one reason why you should read the posts in Shapiro's blog.
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iamanatheistandthisiswhy
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4/11/2014 5:53:57 PM
Posted: 2 years ago
At 4/11/2014 3:33:05 PM, Iredia wrote:
At 4/10/2014 8:57:04 AM, iamanatheistandthisiswhy wrote:
At 4/10/2014 8:18:14 AM, Iredia wrote:
At 4/10/2014 3:18:57 AM, iamanatheistandthisiswhy wrote:
At 4/10/2014 1:46:30 AM, Iredia wrote:
It is repeated that the way organisms evolve and speciate is through principal evolutionary mechanisms of random mutations and natural selection. However, in Wikipedia's article on directed mutations it is mentioned that the likes of Cairns advocated for the mutations which occurred when an organism was exposed to certain stresses. Despite, the amount of experimental evidence behind mechanisms in the cell and gene eg mobile genetic elements which are activated when an organism is exposed go certain environments, why are directed/adaptive mutations still overlooked in favor of ranfom mutations ?

Is Cairns not referring to stress causing mutations that can be random anyway? It is a directed mutation in so much that it may affect a specific sight (area) on the gene, however it is still random. I hope this helps.

If I had a little more information to exactly what you were referencing maybe I could be more help.

Read Wikipedia's article on 'adaptive mutations'. Also read James Shapiro's huffpost blog (http:/m.huffpost.com/us/author/james-a-shapiro) for better context.

Okay, I think I get the question now. The answer is no, it is random.

If you have a set of 100 bugs say. If you then expose these bugs to a poison then say 98 of them die. the remaining 2 had a mutation that occurred on the same gene which prevented their death. This does not mean the mutation happened at the gene because it was directed. It just happens that random mutation is the mutation that provides resistance to the poison. If it was directed then all 100 bugs would survive as the poison would make all the bugs mutate at the same place on the same gene.

Hope that helps.

I'm sure you didn't read Shapiro's blog. You should know that cell signalling (to help a cell respond to its environment) is part of what is responsible for directing the mutations that enable the survival of the two bugs in your scenario. This is one reason why you should read the posts in Shapiro's blog.

The link was to the author in which I could not find what was referenced.

Regardless the fact remains that if it is directed then all the animals should survive as the mutations which would occur at that specific site (directed) would give resistance. If not, then the mutations are not directed right?
Iredia
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4/12/2014 11:38:56 AM
Posted: 2 years ago
At 4/11/2014 5:53:57 PM, iamanatheistandthisiswhy wrote:


The link was to the author in which I could not find what was referenced.

Regardless the fact remains that if it is directed then all the animals should survive as the mutations which would occur at that specific site (directed) would give resistance. If not, then the mutations are not directed right?

Adaptability varies with individuals. This is quite obvious in the case of diseases and how humans (and their immune system) respond to it with some degree of dissmilarity. If you scrolled down further in the page I linked you would have seen the articles I'm referring too. The case, I'm making is the same Shapiro is making: that is many examples of evolution aren't based on random mutations but directed mutations. Sometimes its even random mutations which are directed to a very specific portion of the genome.
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iamanatheistandthisiswhy
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4/12/2014 6:10:07 PM
Posted: 2 years ago
At 4/12/2014 11:38:56 AM, Iredia wrote:
At 4/11/2014 5:53:57 PM, iamanatheistandthisiswhy wrote:


The link was to the author in which I could not find what was referenced.

Regardless the fact remains that if it is directed then all the animals should survive as the mutations which would occur at that specific site (directed) would give resistance. If not, then the mutations are not directed right?

Adaptability varies with individuals. This is quite obvious in the case of diseases and how humans (and their immune system) respond to it with some degree of dissmilarity. If you scrolled down further in the page I linked you would have seen the articles I'm referring too. The case, I'm making is the same Shapiro is making: that is many examples of evolution aren't based on random mutations but directed mutations.
Sometimes its even random mutations which are directed to a very specific portion of the genome.

The bold the part of you argument that is very important, as it is still random. This is the key point.
Iredia
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4/12/2014 6:18:34 PM
Posted: 2 years ago
At 4/12/2014 6:10:07 PM, iamanatheistandthisiswhy wrote:
At 4/12/2014 11:38:56 AM, Iredia wrote:
At 4/11/2014 5:53:57 PM, iamanatheistandthisiswhy wrote:


The link was to the author in which I could not find what was referenced.

Regardless the fact remains that if it is directed then all the animals should survive as the mutations which would occur at that specific site (directed) would give resistance. If not, then the mutations are not directed right?

Adaptability varies with individuals. This is quite obvious in the case of diseases and how humans (and their immune system) respond to it with some degree of dissmilarity. If you scrolled down further in the page I linked you would have seen the articles I'm referring too. The case, I'm making is the same Shapiro is making: that is many examples of evolution aren't based on random mutations but directed mutations.
Sometimes its even random mutations which are directed to a very specific portion of the genome.

The bold the part of you argument that is very important, as it is still random. This is the key point.

All my argument is key. You should know that a random process can be tagged to a directed one eg shuffling music tracks. Its a random sorting through music tracks, but it is directed in part by being restricted to a particular context in an OS.
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iamanatheistandthisiswhy
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4/12/2014 6:45:32 PM
Posted: 2 years ago
At 4/12/2014 6:18:34 PM, Iredia wrote:
At 4/12/2014 6:10:07 PM, iamanatheistandthisiswhy wrote:
At 4/12/2014 11:38:56 AM, Iredia wrote:
At 4/11/2014 5:53:57 PM, iamanatheistandthisiswhy wrote:


The link was to the author in which I could not find what was referenced.

Regardless the fact remains that if it is directed then all the animals should survive as the mutations which would occur at that specific site (directed) would give resistance. If not, then the mutations are not directed right?

Adaptability varies with individuals. This is quite obvious in the case of diseases and how humans (and their immune system) respond to it with some degree of dissmilarity. If you scrolled down further in the page I linked you would have seen the articles I'm referring too. The case, I'm making is the same Shapiro is making: that is many examples of evolution aren't based on random mutations but directed mutations.
Sometimes its even random mutations which are directed to a very specific portion of the genome.

The bold the part of you argument that is very important, as it is still random. This is the key point.

All my argument is key. You should know that a random process can be tagged to a directed one eg shuffling music tracks. Its a random sorting through music tracks, but it is directed in part by being restricted to a particular context in an OS.

The problem is it is directed, but it is still not directed in the sense that the mutation is not happening at the exact same place with the exact same mutation. Hence random.

For example it the DNA sequence is AGTCAGTCAGTC and if any mutation occur then it give immunity. then both AGTXAGTCAGTC and AGTCAGTCXGTC give immunity, but the mutation is different i.e random. Thats why I am saying the word directed is not accurate as it implies something which is deceiving.
tkubok
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4/12/2014 9:21:20 PM
Posted: 2 years ago
At 4/10/2014 1:46:30 AM, Iredia wrote:
It is repeated that the way organisms evolve and speciate is through principal evolutionary mechanisms of random mutations and natural selection. However, in Wikipedia's article on directed mutations it is mentioned that the likes of Cairns advocated for the mutations which occurred when an organism was exposed to certain stresses. Despite, the amount of experimental evidence behind mechanisms in the cell and gene eg mobile genetic elements which are activated when an organism is exposed go certain environments, why are directed/adaptive mutations still overlooked in favor of ranfom mutations ?

Mostly because a) the evidence and experimental results we have that demonstrate that mutations are random, is far far far far far far higher than those that demonstrate adaptive mutations, and b) ultimately, it appears as though it is inconsequential to evolution as a whole.

I mean, what is the ratio of random mutations vs directed/adaptive mutations in nature? What is the ratio of those two mutations in the past that are responsible for benefitial mutations? Does the fact that it responded to stress, necessarily mean that the mutation itself wasnt random, in terms of type and which base pairs were swapped? We already know that there are mutational hotspots, and locations and chemical properties that necessariliy make mutations more likely, such as methylated cytidine.
tkubok
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4/12/2014 9:23:15 PM
Posted: 2 years ago
At 4/12/2014 11:38:56 AM, Iredia wrote:
At 4/11/2014 5:53:57 PM, iamanatheistandthisiswhy wrote:


The link was to the author in which I could not find what was referenced.

Regardless the fact remains that if it is directed then all the animals should survive as the mutations which would occur at that specific site (directed) would give resistance. If not, then the mutations are not directed right?

Adaptability varies with individuals. This is quite obvious in the case of diseases and how humans (and their immune system) respond to it with some degree of dissmilarity. If you scrolled down further in the page I linked you would have seen the articles I'm referring too. The case, I'm making is the same Shapiro is making: that is many examples of evolution aren't based on random mutations but directed mutations. Sometimes its even random mutations which are directed to a very specific portion of the genome.

So, wait, are you saying that the immune system response is what you would call Directed mutation?
Iredia
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4/13/2014 1:57:42 AM
Posted: 2 years ago
At 4/12/2014 9:23:15 PM, tkubok wrote:
At 4/12/2014 11:38:56 AM, Iredia wrote:
At 4/11/2014 5:53:57 PM, iamanatheistandthisiswhy wrote:


The link was to the author in which I could not find what was referenced.

Regardless the fact remains that if it is directed then all the animals should survive as the mutations which would occur at that specific site (directed) would give resistance. If not, then the mutations are not directed right?

Adaptability varies with individuals. This is quite obvious in the case of diseases and how humans (and their immune system) respond to it with some degree of dissmilarity. If you scrolled down further in the page I linked you would have seen the articles I'm referring too. The case, I'm making is the same Shapiro is making: that is many examples of evolution aren't based on random mutations but directed mutations. Sometimes its even random mutations which are directed to a very specific portion of the genome.

So, wait, are you saying that the immune system response is what you would call Directed mutation?

Yes. I would back that up with a few peer-reviewed papers and quotes from them. I might also post Youtube videos.
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Iredia
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4/13/2014 2:58:47 AM
Posted: 2 years ago
At 4/12/2014 6:45:32 PM, iamanatheistandthisiswhy wrote:


The problem is it is directed, but it is still not directed in the sense that the mutation is not happening at the exact same place with the exact same mutation. Hence random.

For example it the DNA sequence is AGTCAGTCAGTC and if any mutation occur then it give immunity. then both AGTXAGTCAGTC and AGTCAGTCXGTC give immunity, but the mutation is different i.e random. Thats why I am saying the word directed is not accurate as it implies something which is deceiving.

It is. For example, the mutations which help confer immunity on new diseases humans encounter and neutralize occur in specific gene regions in specific cells which hypermutate (ie mutate at a rate far above normal). An enzyme involved has been suggested. Read this article: http://en.wikipedia.org...
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slo1
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4/13/2014 10:36:21 AM
Posted: 2 years ago
There really is no such thing as a random mutation. It has to have an environmental cause to change, add, or delete the base pair. We simply call it random because we are not looking at a micro level to explain exactly how the mutation formed.
tkubok
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4/13/2014 6:08:35 PM
Posted: 2 years ago
At 4/13/2014 1:57:42 AM, Iredia wrote:
At 4/12/2014 9:23:15 PM, tkubok wrote:
At 4/12/2014 11:38:56 AM, Iredia wrote:
At 4/11/2014 5:53:57 PM, iamanatheistandthisiswhy wrote:


The link was to the author in which I could not find what was referenced.

Regardless the fact remains that if it is directed then all the animals should survive as the mutations which would occur at that specific site (directed) would give resistance. If not, then the mutations are not directed right?

Adaptability varies with individuals. This is quite obvious in the case of diseases and how humans (and their immune system) respond to it with some degree of dissmilarity. If you scrolled down further in the page I linked you would have seen the articles I'm referring too. The case, I'm making is the same Shapiro is making: that is many examples of evolution aren't based on random mutations but directed mutations. Sometimes its even random mutations which are directed to a very specific portion of the genome.

So, wait, are you saying that the immune system response is what you would call Directed mutation?

Yes. I would back that up with a few peer-reviewed papers and quotes from them. I might also post Youtube videos.

I understand the mechanism with regards to the immune system response, fairly well.

What I dont understand is why this isnt random mutation or natural selection.

As I said in the comment before the one you responded to, we understand very well that places in the geneome with Methylated Cytidine have a higher chance of mutation.

But whether the mutation occurs is ultimately useful, isnt something that is gaurunteed, and is infact random. The type of mutation, the effects, whether it is benefitial or not, all of this is random. And when a benifitial mutation occurs, natural selection selects for it.

I dont think that scientists are claiming that random mutations are distributed evenly across the genome, that there are no external factors that determine the likelihood of whether a mutation occurs in a specific spot rather than a random spot in the genome.
iamanatheistandthisiswhy
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4/14/2014 12:28:52 AM
Posted: 2 years ago
At 4/13/2014 2:58:47 AM, Iredia wrote:
At 4/12/2014 6:45:32 PM, iamanatheistandthisiswhy wrote:


The problem is it is directed, but it is still not directed in the sense that the mutation is not happening at the exact same place with the exact same mutation. Hence random.

For example it the DNA sequence is AGTCAGTCAGTC and if any mutation occur then it give immunity. then both AGTXAGTCAGTC and AGTCAGTCXGTC give immunity, but the mutation is different i.e random. Thats why I am saying the word directed is not accurate as it implies something which is deceiving.

It is. For example, the mutations which help confer immunity on new diseases humans encounter and neutralize occur in specific gene regions in specific cells which hypermutate (ie mutate at a rate far above normal). An enzyme involved has been suggested. Read this article: http://en.wikipedia.org...

So what you are saying then is that these two sequences are the same?
AGTXAGTCAGTC and AGTCAGTCXGTC
Iredia
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4/14/2014 2:09:26 AM
Posted: 2 years ago
At 4/14/2014 12:28:52 AM, iamanatheistandthisiswhy wrote:
At 4/13/2014 2:58:47 AM, Iredia wrote:
At 4/12/2014 6:45:32 PM, iamanatheistandthisiswhy wrote:


The problem is it is directed, but it is still not directed in the sense that the mutation is not happening at the exact same place with the exact same mutation. Hence random.

For example it the DNA sequence is AGTCAGTCAGTC and if any mutation occur then it give immunity. then both AGTXAGTCAGTC and AGTCAGTCXGTC give immunity, but the mutation is different i.e random. Thats why I am saying the word directed is not accurate as it implies something which is deceiving.

It is. For example, the mutations which help confer immunity on new diseases humans encounter and neutralize occur in specific gene regions in specific cells which hypermutate (ie mutate at a rate far above normal). An enzyme involved has been suggested. Read this article: http://en.wikipedia.org...

So what you are saying then is that these two sequences are the same?
AGTXAGTCAGTC and AGTCAGTCXGTC

No, I'm not saying that. I'm pointing out OTOH that the mutations (of part of the immune system) are dirceted by enzymes and repeatedly occur in a give part tha can tolerate such hypermutations. Did you read the link at all ? Because adaptive mutation is too much of a fact to be discounted.
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Iredia
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4/14/2014 2:13:54 AM
Posted: 2 years ago
At 4/13/2014 10:36:21 AM, slo1 wrote:
There really is no such thing as a random mutation. It has to have an environmental cause to change, add, or delete the base pair. We simply call it random because we are not looking at a micro level to explain exactly how the mutation formed.

Random mutations are accidental mutations caused by toxic chemicals, UV rays or mistakes in DNA replication.
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Iredia
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4/14/2014 2:42:53 AM
Posted: 2 years ago
At 4/13/2014 6:08:35 PM, tkubok wrote:

I understand the mechanism with regards to the immune system response, fairly well.

What I dont understand is why this isnt random mutation or natural selection.

As I said in the comment before the one you responded to, we understand very well that places in the geneome with Methylated Cytidine have a higher chance of mutation.

But whether the mutation occurs is ultimately useful, isnt something that is gaurunteed, and is infact random. The type of mutation, the effects, whether it is benefitial or not, all of this is random. And when a benifitial mutation occurs, natural selection selects for it.

I dont think that scientists are claiming that random mutations are distributed evenly across the genome, that there are no external factors that determine the likelihood of whether a mutation occurs in a specific spot rather than a random spot in the genome.

It isn't random mutation because the genes responsible for combating antibodies are very specific and also specific in where they can tolerate the mutations which fight antibodies. Your body (and pharmaceutical companies) can't afford to sit around for beneficial random mutations to occur, survive and thrive, and be forged over deep time to fight a deadly disease. They have to (and actually) work on them ASAP. It is well-known and taught that the human body's adaptive immune system even has a sort of memory and database where succesful antigens for diseases are stored so they may be utilized again. Does that even sound like a random process ? Furthermore, see what Wikipedia's article on somatic hypermutations writes, "Somatic hypermutation involves a PROGRAMMED PROCESS of mutation affecting the variable regions of immunoglobulin genes. Unlike germline mutation, SHM affects only individual immune cells, and the mutations are not transmitted to offspring." Even then genetic recombination in germ cells and in zygotes are directed. Trying to plug in random mutations in those processes mostly gets you deformities.
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iamanatheistandthisiswhy
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4/14/2014 2:51:47 AM
Posted: 2 years ago
At 4/14/2014 2:09:26 AM, Iredia wrote:
At 4/14/2014 12:28:52 AM, iamanatheistandthisiswhy wrote:
At 4/13/2014 2:58:47 AM, Iredia wrote:
At 4/12/2014 6:45:32 PM, iamanatheistandthisiswhy wrote:


The problem is it is directed, but it is still not directed in the sense that the mutation is not happening at the exact same place with the exact same mutation. Hence random.

For example it the DNA sequence is AGTCAGTCAGTC and if any mutation occur then it give immunity. then both AGTXAGTCAGTC and AGTCAGTCXGTC give immunity, but the mutation is different i.e random. Thats why I am saying the word directed is not accurate as it implies something which is deceiving.

It is. For example, the mutations which help confer immunity on new diseases humans encounter and neutralize occur in specific gene regions in specific cells which hypermutate (ie mutate at a rate far above normal). An enzyme involved has been suggested. Read this article: http://en.wikipedia.org...

So what you are saying then is that these two sequences are the same?
AGTXAGTCAGTC and AGTCAGTCXGTC

No, I'm not saying that. I'm pointing out OTOH that the mutations (of part of the immune system) are dirceted by enzymes and repeatedly occur in a give part tha can tolerate such hypermutations. Did you read the link at all ? Because adaptive mutation is too much of a fact to be discounted.

Ok, so they occur in a given part. Part is not the same as single site. So let me try give another example using sequences.
ABCDABCDABCD - normal
ABCFABCDABCD - resistance
ABCDAFCDABCD - resistance
ABCDFBCDABCD - no resistance

All the same part, but the site is random and hence the outcome is random.
tkubok
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4/14/2014 12:53:44 PM
Posted: 2 years ago
At 4/14/2014 2:42:53 AM, Iredia wrote:
At 4/13/2014 6:08:35 PM, tkubok wrote:

I understand the mechanism with regards to the immune system response, fairly well.

What I dont understand is why this isnt random mutation or natural selection.

As I said in the comment before the one you responded to, we understand very well that places in the geneome with Methylated Cytidine have a higher chance of mutation.

But whether the mutation occurs is ultimately useful, isnt something that is gaurunteed, and is infact random. The type of mutation, the effects, whether it is benefitial or not, all of this is random. And when a benifitial mutation occurs, natural selection selects for it.

I dont think that scientists are claiming that random mutations are distributed evenly across the genome, that there are no external factors that determine the likelihood of whether a mutation occurs in a specific spot rather than a random spot in the genome.

It isn't random mutation because the genes responsible for combating antibodies are very specific and also specific in where they can tolerate the mutations which fight antibodies.

What do you mean by "Where they can tolerate the mutations"? A huge portion of the DNA can tolerate mutations, which is why most mutations are silent.

Your body (and pharmaceutical companies) can't afford to sit around for beneficial random mutations to occur, survive and thrive, and be forged over deep time to fight a deadly disease.

...As opposed to succumbing to your disease and dying, like many many many millions have?

I mean, what youre discussing here is a chemical pathway. But this has nothing to do with mutations. When I cut my finger, blood starts to clot at the wound. It would be detrimental if the blood clotted all over my body, or if it never clotted at all. But blood clotting, is a specific reaction that involves no mutation whatsoever. Chemical pathways like these, already exist, regardless of whether they contain mutations or not.

They have to (and actually) work on them ASAP. It is well-known and taught that the human body's adaptive immune system even has a sort of memory and database where succesful antigens for diseases are stored so they may be utilized again. Does that even sound like a random process ?

Since the memory database takes the form of letting past antibodies freefloat around, that really doesnt have anything to do with whether this is a random process or not.

Furthermore, see what Wikipedia's article on somatic hypermutations writes, "Somatic hypermutation involves a PROGRAMMED PROCESS of mutation affecting the variable regions of immunoglobulin genes. Unlike germline mutation, SHM affects only individual immune cells, and the mutations are not transmitted to offspring." Even then genetic recombination in germ cells and in zygotes are directed. Trying to plug in random mutations in those processes mostly gets you deformities.

Did you not read what I posted, before?

"But whether the mutation occurs is ultimately useful, isnt something that is gaurunteed, and is infact random. The type of mutation, the effects, whether it is benefitial or not, all of this is random. And when a benifitial mutation occurs, natural selection selects for it."

So basically the Mutation is random, but the location of the mutation is not?
Iredia
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4/17/2014 6:39:19 AM
Posted: 2 years ago
@ tkubok: Your points don't address mine. Take for example, my point that genes for the immune system are specific in where they tolerate mutations. You simply assert that huge parts of the DNA, as if that excuses the point I made, or that Hox genes are another gene set very well conserved. If a mutation is adaptive or directed there would be systems which enable it sense changes in its environment and respond appropriately. Now, we know about signal transduction pathways and how they interact with gene regulatory networks to direct mutation in certain conditions. @ iamanatheistandthisiswhy The site of hypermutatiins in the adaptive immune system is specific not random. Read the link I posted.
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iamanatheistandthisiswhy
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4/18/2014 12:26:09 AM
Posted: 2 years ago
At 4/17/2014 6:39:19 AM, Iredia wrote:
@ tkubok: Your points don't address mine. Take for example, my point that genes for the immune system are specific in where they tolerate mutations. You simply assert that huge parts of the DNA, as if that excuses the point I made, or that Hox genes are another gene set very well conserved. If a mutation is adaptive or directed there would be systems which enable it sense changes in its environment and respond appropriately. Now, we know about signal transduction pathways and how they interact with gene regulatory networks to direct mutation in certain conditions. @ iamanatheistandthisiswhy The site of hypermutatiins in the adaptive immune system is specific not random. Read the link I posted.

OK, firstly Wikipedia is not the greatest source to cite. But if you read it then you will understand that they are talking about random mutations in specific repeat sections and not a specific directed mutation.

Look at the example below, this is what the link is saying.
i.e. ABABABABABABABABA -normal
ABABABABABAcABABA - mutation
ABAcABABABABABABA -mutation
The mutations are in the same site, but still random. This is what I have been saying since the beginning. To say it is directed and the same then you have to accept that the two mutation sequences shown above are the exact same, and this is clearly illogical.
tkubok
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4/18/2014 9:49:49 AM
Posted: 2 years ago
At 4/17/2014 6:39:19 AM, Iredia wrote:
@ tkubok: Your points don't address mine.

Yes, they do. You said, in the beginning, as to why scientists overlook adaptive mutations in favor of random mutations. And yet I demonstrated how the mutation aspect of this was still random. There is nothing within random mutations that necessitates that the mutation occur at a random location, all that is required is the ultimate benefit or detriment to be random.

I addressed your original concern, your original argument, your original point that you made in the very first comment of this topic. And yet you havent even discussed that yet.

Take for example, my point that genes for the immune system are specific in where they tolerate mutations.

So I ask you what you mean by "Able to tolerate mutations", and you come back with "they are able to tolerate mutations."

And then you say that my points dont address yours.

Did you even read what I wrote? Im pretty sure that asking you to clarify on the point that you made, is addressing the point that you made.

You simply assert that huge parts of the DNA, as if that excuses the point I made, or that Hox genes are another gene set very well conserved.

I assert that huge parts of the DNA.... do what, exactly? Your sentence is incomplete. And I dont think i ever mentioned Hox genes, at all.

If a mutation is adaptive or directed there would be systems which enable it sense changes in its environment and respond appropriately.

This is why I demonstrated that changes that are specific to certain stimuli have nothing to do with Mutations, and therefore, specifically with examples within the human body, where the pathways already exist that allow reaction to certain stimuli and stresses, like blood clotting in response to cuts, shows how the human body is already built to react to stimuli.

Now, we know about signal transduction pathways and how they interact with gene regulatory networks to direct mutation in certain conditions.

Sure. But none of this is specifically exclusive to mutations.

So, we have a couple dozen examples of changes that occur that are in response to specific stimuli and stresses in the body.

And one of those, includes mutations.

What exactly is the argument youre trying to make here? This adaptive mutation as you call it seems to be the result of a long chain of evolution and random mutation that produced a system where mutations occur because of a certain stimuli. Is this what you wanted to demonstrate?
Enji
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4/18/2014 11:58:25 AM
Posted: 2 years ago
At 4/13/2014 2:58:47 AM, Iredia wrote:
At 4/12/2014 6:45:32 PM, iamanatheistandthisiswhy wrote:

The problem is it is directed, but it is still not directed in the sense that the mutation is not happening at the exact same place with the exact same mutation. Hence random.

For example it the DNA sequence is AGTCAGTCAGTC and if any mutation occur then it give immunity. then both AGTXAGTCAGTC and AGTCAGTCXGTC give immunity, but the mutation is different i.e random. Thats why I am saying the word directed is not accurate as it implies something which is deceiving.

It is. For example, the mutations which help confer immunity on new diseases humans encounter and neutralize occur in specific gene regions in specific cells which hypermutate (ie mutate at a rate far above normal). An enzyme involved has been suggested. Read this article: http://en.wikipedia.org...

I think you and iamanathiestandthisiswhy agree more than you think. Mutations are undeniably stochastic. This doesn't mean that there's an equal probability of each mutation everywhere, but it does mean that environmental stresses don't deterministically cause DNA to rearrange in the specific pattern which confers resistance to those environmental stresses. This is why a higher rate of mutation is important; a single mutation granting resistance is equally likely, but with more frequent mutations cells will be able to respond to environmental stress sooner.

The problem with adaptive, acquired mutations is that they affect an organism's somatic cells, but only germline mutations are inherited by offspring. And if the mutations aren't inherited by offspring, then they are irrelevant to evolution.
Idealist
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4/18/2014 10:45:45 PM
Posted: 2 years ago
At 4/11/2014 3:33:05 PM, Iredia wrote:
At 4/10/2014 8:57:04 AM, iamanatheistandthisiswhy wrote:
At 4/10/2014 8:18:14 AM, Iredia wrote:
At 4/10/2014 3:18:57 AM, iamanatheistandthisiswhy wrote:
At 4/10/2014 1:46:30 AM, Iredia wrote:
It is repeated that the way organisms evolve and speciate is through principal evolutionary mechanisms of random mutations and natural selection. However, in Wikipedia's article on directed mutations it is mentioned that the likes of Cairns advocated for the mutations which occurred when an organism was exposed to certain stresses. Despite, the amount of experimental evidence behind mechanisms in the cell and gene eg mobile genetic elements which are activated when an organism is exposed go certain environments, why are directed/adaptive mutations still overlooked in favor of ranfom mutations ?

Is Cairns not referring to stress causing mutations that can be random anyway? It is a directed mutation in so much that it may affect a specific sight (area) on the gene, however it is still random. I hope this helps.

If I had a little more information to exactly what you were referencing maybe I could be more help.

Read Wikipedia's article on 'adaptive mutations'. Also read James Shapiro's huffpost blog (http:/m.huffpost.com/us/author/james-a-shapiro) for better context.

Okay, I think I get the question now. The answer is no, it is random.

If you have a set of 100 bugs say. If you then expose these bugs to a poison then say 98 of them die. the remaining 2 had a mutation that occurred on the same gene which prevented their death. This does not mean the mutation happened at the gene because it was directed. It just happens that random mutation is the mutation that provides resistance to the poison. If it was directed then all 100 bugs would survive as the poison would make all the bugs mutate at the same place on the same gene.

Hope that helps.

I'm sure you didn't read Shapiro's blog. You should know that cell signalling (to help a cell respond to its environment) is part of what is responsible for directing the mutations that enable the survival of the two bugs in your scenario. This is one reason why you should read the posts in Shapiro's blog.

I haven't read the sources you cited, but I have studied material about the importance of cell signaling. For example, cells in the body are usually signaled when it is beneficial for them to die, and they must respond to this without question in order for the larger organism to maintain its health. If cells didn't die as directed then a person would end-up weighing tons before they were ten-years-old. No one really understands yet the methodology of this extremely complex process. Too many people seem to think that all intelligence lies within the brain, but the brain is only part of the CNS, and the CNS is only part of the nervous system as a whole. Not all animals even have brains. We know that things such as "muscle memory" exist, which is why we practice using repetition, but we don't understand how the body works as a complete "knowing' organism. For example, why does a finger or toe feel as much a part of us as the mind itself? Eastern philosophies have always thought of the body as one singular being, while Western medicine has seemed to try separating us into a brain which contains who we are and a body which serves the brain. My guess is that we'll eventually find answers which lie somewhere in-between.
Iredia
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4/19/2014 2:17:29 PM
Posted: 2 years ago
At 4/18/2014 10:45:45 PM, Idealist wrote:

I haven't read the sources you cited, but I have studied material about the importance of cell signaling. For example, cells in the body are usually signaled when it is beneficial for them to die, and they must respond to this without question in order for the larger organism to maintain its health. If cells didn't die as directed then a person would end-up weighing tons before they were ten-years-old. No one really understands yet the methodology of this extremely complex process. Too many people seem to think that all intelligence lies within the brain, but the brain is only part of the CNS, and the CNS is only part of the nervous system as a whole. Not all animals even have brains. We know that things such as "muscle memory" exist, which is why we practice using repetition, but we don't understand how the body works as a complete "knowing' organism. For example, why does a finger or toe feel as much a part of us as the mind itself? Eastern philosophies have always thought of the body as one singular being, while Western medicine has seemed to try separating us into a brain which contains who we are and a body which serves the brain. My guess is that we'll eventually find answers which lie somewhere in-between.

Here's a third way Shapiro proposes. He calls it 'natural genetic engineering'. new.bostonreview.net/BR22.1/shapiro.html I thinks it's an interesting take and I agree with it. However, I still think it begs the question of design or evolution. And Jerry Coyne's response for some balance: http://whyevolutionistrue.wordpress.com...
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Idealist
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4/19/2014 5:16:03 PM
Posted: 2 years ago
At 4/19/2014 2:17:29 PM, Iredia wrote:
At 4/18/2014 10:45:45 PM, Idealist wrote:

I haven't read the sources you cited, but I have studied material about the importance of cell signaling. For example, cells in the body are usually signaled when it is beneficial for them to die, and they must respond to this without question in order for the larger organism to maintain its health. If cells didn't die as directed then a person would end-up weighing tons before they were ten-years-old. No one really understands yet the methodology of this extremely complex process. Too many people seem to think that all intelligence lies within the brain, but the brain is only part of the CNS, and the CNS is only part of the nervous system as a whole. Not all animals even have brains. We know that things such as "muscle memory" exist, which is why we practice using repetition, but we don't understand how the body works as a complete "knowing' organism. For example, why does a finger or toe feel as much a part of us as the mind itself? Eastern philosophies have always thought of the body as one singular being, while Western medicine has seemed to try separating us into a brain which contains who we are and a body which serves the brain. My guess is that we'll eventually find answers which lie somewhere in-between.

Here's a third way Shapiro proposes. He calls it 'natural genetic engineering'. new.bostonreview.net/BR22.1/shapiro.html I thinks it's an interesting take and I agree with it. However, I still think it begs the question of design or evolution. And Jerry Coyne's response for some balance: http://whyevolutionistrue.wordpress.com...

Definitely an interesting article. I plan to go back and read it more closely when I get the time.