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Author Topic:   The Nature of Mutations
PhospholipidGen
Inactive Member


Message 1 of 344 (36819)
04-12-2003 1:44 AM


The nature of mutations have been discovered to be changes in amino acid sequences during the replication of DNA. This includes additions, deletions and substitutions of those amino acids which may have an effect upon the protein that is being synthesized.
Mutations fall into two main catagories depending upon their phenotypic effects, they are neutral and deleterious. There is no such catagory for "beneficial" mutations in reality, for a very good reason. The term "beneficial mutation" can only be defined according to the organism and the environment to which it is applied, it has absolutely nothing to do with the mutation itself.
Mutations that confer "beneficial" effects upon the affected organism are still deleterious mutations. The fact that they may in some small way give an organism some degree of solice in its environment does not change the fact of the nature of the mutation.
Evolutionary theorists favorite mutation to quibble about is the sickle cell anemia mutation...this is a deleterious mutation by catagory. It damages the cells to the point that they cannot function as they were intedned to function, they have been damaged. True, that in certain areas this gives the seeming benefit of conferring "resistance" to those affected with the mutation, but this does not erase the damage that the person sustains due to that mutation.
Second, it has not been proven anywhere at any time to my knowledge that variation arises from mutations. This is part of the grand assumption that evolution is a fact and, therefore, the naturalistic paradigm demands endless variational changes, so theorists assume it into the equation. This is why it is called a "gene pool" and not a "gene stream" because there is NOT an endless supply of variation streaming into the genome of species.
Without endless variation, you have no evolutionary change. Adaptational changes in organisms are due to changes in gene expression by environmental ques, and are not due to mutations.
All of your examples of bacterial adaptation that I have come across to date are just that, changes in gene expression, from inactivated to activated sites. Nothing more. I also find it hilarious that after touting that evolutionary change takes hundreds of thousands of years to take hold, now suddenly we can take a bacteria and bring about evolutionary changes in months. This is not evolutionary change, this is adaptation.
And adaptation is not evolution, it is not speciation. It is change, but if you are going to go to that silly and ridiculous length to try to prove evolutioanry theory, then we better start calling every single kind of change in the all of all as evolution.
Gotta go, looking forward to your comments.
Have a nice weekend!

Replies to this message:
 Message 2 by NosyNed, posted 04-12-2003 2:30 AM PhospholipidGen has replied
 Message 3 by NosyNed, posted 04-12-2003 2:49 AM PhospholipidGen has replied
 Message 4 by Sylas, posted 04-12-2003 3:27 AM PhospholipidGen has replied
 Message 5 by Brad McFall, posted 04-12-2003 2:25 PM PhospholipidGen has not replied
 Message 8 by crashfrog, posted 04-12-2003 4:26 PM PhospholipidGen has replied
 Message 14 by Coragyps, posted 04-13-2003 10:37 AM PhospholipidGen has replied
 Message 15 by Paul, posted 04-14-2003 1:12 PM PhospholipidGen has replied
 Message 44 by Gzus, posted 04-21-2003 8:00 AM PhospholipidGen has not replied

NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 2 of 344 (36822)
04-12-2003 2:30 AM
Reply to: Message 1 by PhospholipidGen
04-12-2003 1:44 AM


New Genes for old
quote:
changes in gene expression, from inactivated to activated sites. Nothing more.
So if there was a specific example of a mutation that was not there to be activated but occured by chance and that mutation confered benefit then you'd be wrong in your assertions?
Just to clarify: You're saying that all beneficial mutations are a result of a gene activation? But you will agree that there are "real" mutations (that is genetic changes which were not there at all before)?
What stops the "real" mutations from ever being beneficial?
What causes the gene to be activated when needed?
[This message has been edited by NosyNed, 04-12-2003]

This message is a reply to:
 Message 1 by PhospholipidGen, posted 04-12-2003 1:44 AM PhospholipidGen has replied

Replies to this message:
 Message 25 by PhospholipidGen, posted 04-20-2003 4:42 PM NosyNed has not replied

NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 3 of 344 (36824)
04-12-2003 2:49 AM
Reply to: Message 1 by PhospholipidGen
04-12-2003 1:44 AM


Nothing to do with a mutation
quote:
Mutations that confer "beneficial" effects upon the affected organism are still deleterious mutations. The fact that they may in some small way give an organism some degree of solice in its environment does not change the fact of the nature of the mutation.
Your example of the sickle cell mutation is one which has both deleterious effects and beneficial ones. OK.
Are you saying in the above that if there was any mutation that didn't have the deleterious side effect that the sickle cell mutation does that it would still not be "beneficial"? How could you say that?
Or do you mean that you don't think there can be any such mutation that while beneficial don't also have some deleterious effect?

This message is a reply to:
 Message 1 by PhospholipidGen, posted 04-12-2003 1:44 AM PhospholipidGen has replied

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Sylas
Member (Idle past 5261 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 4 of 344 (36825)
04-12-2003 3:27 AM
Reply to: Message 1 by PhospholipidGen
04-12-2003 1:44 AM


PhospholipidGen writes:
The nature of mutations have been discovered to be changes in amino acid sequences during the replication of DNA. This includes additions, deletions and substitutions of those amino acids which may have an effect upon the protein that is being synthesized.
Some minor technical errors here. Mutation is change in the sequence of base pairs of DNA. This can be addition, deletion, substitution, and also translations; in which a segment of DNA is reversed or moved from one place to another. There are also some gross chomosomal mutations, which need not concern us.
One of the most important functions of DNA is to synthesize proteins, and it is proteins which are made up of amino acid sequences. So a mutation in DNA can have a carry over effect in synthesized proteins. But it can also disable any expression at all of some protein, or introduce a new protein altogether, by mutation of the basepair sequences to introduce or remove the start codon which makrs the point in DNA where protein expression begins.
This is all just a matter of getting the terminology correct and understanding the difference between DNA, and basepair, and amino acid, and protein, and so on.
Mutations fall into two main catagories depending upon their phenotypic effects, they are neutral and deleterious. There is no such catagory for "beneficial" mutations in reality, for a very good reason. The term "beneficial mutation" can only be defined according to the organism and the environment to which it is applied, it has absolutely nothing to do with the mutation itself.
The qualification you make for "beneficial" applies just as much for deleterious. Suppose you have a mutation which you are willing to label as deleterious. What do you call a mutation which reverses the deleterious mutation?
Evolutionary theorists favorite mutation to quibble about is the sickle cell anemia mutation...this is a deleterious mutation by catagory. It damages the cells to the point that they cannot function as they were intedned to function, they have been damaged. True, that in certain areas this gives the seeming benefit of conferring "resistance" to those affected with the mutation, but this does not erase the damage that the person sustains due to that mutation.
You miss the point. The mutation has some effects which are beneficial, and other effects which are detrimental. How, then, can you label it as deleterious? There are some environments in which it is a benefit.
(There is a subtle point here also, in that the major deleterious effect is in homozygotes for the mutated allele.)
What this demonstrates is that beneficial and deleterious are both defined with respect to an environment.
Second, it has not been proven anywhere at any time to my knowledge that variation arises from mutations. This is part of the grand assumption that evolution is a fact and, therefore, the naturalistic paradigm demands endless variational changes, so theorists assume it into the equation. This is why it is called a "gene pool" and not a "gene stream" because there is NOT an endless supply of variation streaming into the genome of species.
This is merely berwildering. What do you think variation means? Of course mutations lead the variation. How could they not? Mutations occur all the time. This is observed. We both probably have around 60 mutations which were not in our parents, and a couple of those are not silent, having an effect on the amin acid sequences of expressed proteins. And there are even more mutations difference with your grandparents, of course. Etc. This is not an assumption. This is an observation.
All of your examples of bacterial adaptation that I have come across to date are just that, changes in gene expression, from inactivated to activated sites. Nothing more. I also find it hilarious that after touting that evolutionary change takes hundreds of thousands of years to take hold, now suddenly we can take a bacteria and bring about evolutionary changes in months. This is not evolutionary change, this is adaptation.
It is a repeatable experiment to observe that mutations arise in bacterial cultures, and that advantageous mutations get selected, and the result is a population in which new mutations become fixed. This is not a change from active to inactive sites. It is (for example) a change in the sequences of DNA, and hence in the sequences of expressed proteins. You even define it above more or less appropriately, if we skip over the minor confusion between a sequence of basepairs in DNA, and a sequence of amino acids in proteins.
The mutations change the DNA sequence, which changes the protein sequence, which has an effect, which is sometimes advantageous and hence tends to spread through the bacterial culture as generation pass.
And adaptation is not evolution, it is not speciation. It is change, but if you are going to go to that silly and ridiculous length to try to prove evolutioanry theory, then we better start calling every single kind of change in the all of all as evolution.
Shrug. Any biologically heritable change is evolution, by definition. Give a lot of time, inherited changes accumulate, driving copies further and further from the parent form. Selection is the process which weeds out deleterious changes; the end result is organisms which are different, but which remain adapted. Speciation is what happens when sufficient change has accumulated betwee two populations that they no longer breed together. Once that occurs, the populations simply continue to diverge as time passes.
Sure; a small observed mutation arising in a petri dish and becoming fixed in a bacterial culture is not speciation. It is demonstration of the processes of variation and selection. How are you going to stop change from accumulating over time? We observe the processes involved in evolutionary (inherited) change over small time scales, and we observe the fact changes in lineages over long time scales in the traces they leave behind. We observe the nested patterns of similarity between existing species, and note that it conforms to the patterns produced by cummulative inherited variation.
Cheers -- Chris

This message is a reply to:
 Message 1 by PhospholipidGen, posted 04-12-2003 1:44 AM PhospholipidGen has replied

Replies to this message:
 Message 27 by PhospholipidGen, posted 04-20-2003 5:16 PM Sylas has replied

Brad McFall
Member (Idle past 5033 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 5 of 344 (36837)
04-12-2003 2:25 PM
Reply to: Message 1 by PhospholipidGen
04-12-2003 1:44 AM


expression
But when C Aquadro whom I saw and not his genes appear on the Cornell Campus writes ON THE POSITIVE SIDE OF THE LEDGER, "the fixation of a single nucleotide substitution, however suggestive, provides no statistical power." theis board is left to dangle in the wind.
I have left many clues to be tried but we do not even attempt to be able to think thru them let alone show them to be false (or true) so I will say nothing else. "Background selection" always seemed a slight to me but unless the CAUSE of mutations (by correlation to bioge0grapy for instance were deductively possible (Aquadro's "shape of the genelogy giving demographics') our promotable view of mutations itself also can not make the next go (there was an "or" in this position which may not be an addition but a multiplication. I have no idea but need work from cause not because there is symbolism available.)
The proposal would be for a non-biological overdetermination of mutation categories by BEING thrown into the electrotonic state. Selection is not of the (this) kind. Gould simply could not THINK of someone putting drift and selection to the lack of something elese.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 6 of 344 (36838)
04-12-2003 2:47 PM


Am I just slow
Does the above post actually mean something and it is just too abstruse for me to grasp, or is it just gibberish?

Replies to this message:
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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 7 of 344 (36839)
04-12-2003 2:48 PM
Reply to: Message 5 by Brad McFall
04-12-2003 2:25 PM


translation please
Could you try again? I don't seem to be smart enough or have enough command of the English language to make any sense whatsoever of your post.

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 8 of 344 (36842)
04-12-2003 4:26 PM
Reply to: Message 1 by PhospholipidGen
04-12-2003 1:44 AM


Mutations that confer "beneficial" effects upon the affected organism are still deleterious mutations. The fact that they may in some small way give an organism some degree of solice in its environment does not change the fact of the nature of the mutation.
The utility (or lack of same) of ANY mutation is due to environment. Specifically, the chemical envrionment of the new protein. That includes the chemical envrionment of the cell as well as the environment of the organism.
I don't see how you can just blanketly assert that even beneficial mutations are deleterious. No mutation is inherently good or bad on it's own right. It's only as it relates to the organisms survival in it's envrionment that we can make that judgement.
You call it "damage" because to you, the protein doesn't work as it's "supposed to". Inherent in your view is a kind of platonic idealism, where organisms have some kind of "perfect state" that any deviation from is, by nature, inferior. This is incorrect. For all you've said about biologists assuming things, it's your asusmtions I would take a closer look at if I were you. Just because a sickle-cell heterzygotes cells are "different" doesn't mean they're "broken". In fact, they work just fine. Heterozygotes for this condition lead full lives. And the upshot is the resistance to malaria. The only way you could think this was bad was if you identified "different" as "bad".
Is your entire argument going to center around using terms like "beneficial", "science", and "variation" in ways totally at odds with the english language?
------------------
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This message is a reply to:
 Message 1 by PhospholipidGen, posted 04-12-2003 1:44 AM PhospholipidGen has replied

Replies to this message:
 Message 9 by NosyNed, posted 04-12-2003 7:23 PM crashfrog has replied
 Message 31 by PhospholipidGen, posted 04-20-2003 9:49 PM crashfrog has replied

NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 9 of 344 (36853)
04-12-2003 7:23 PM
Reply to: Message 8 by crashfrog
04-12-2003 4:26 PM


Maybe some are deleterious
I think it is possible to say some specific mutations are deleterious without any reference to the environment.
Remember that some large fractions of all pregnancies spontaniously miscarry. If a mutation is behind a terminated pregnancy then I think it is deleterious independently of the environment it doesn't get to see.

This message is a reply to:
 Message 8 by crashfrog, posted 04-12-2003 4:26 PM crashfrog has replied

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 10 of 344 (36883)
04-13-2003 12:04 AM
Reply to: Message 9 by NosyNed
04-12-2003 7:23 PM


Re: Maybe some are deleterious
I agree that some deleterious (perhaps most) mutations are harmful for reasons that have nothing to do with the organism's environment; but my point was that since the cellular metabolism of the organism is itself the chemical "environment" for proteins, and that protein is beneficial or deleterious based on its interactions with other chemicals and proteins in that environment, one could consider all mutations as being defined in utility by "environment". I realize it's not generally what "environment" refers to, my point was show that the envrionment simply can't be discounted when considering the utility of mutations.
Does that make any sense?
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 Message 9 by NosyNed, posted 04-12-2003 7:23 PM NosyNed has replied

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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 11 of 344 (36884)
04-13-2003 12:10 AM
Reply to: Message 10 by crashfrog
04-13-2003 12:04 AM


Re: Maybe some are deleterious
quote:
Does that make any sense?
Yes, I think so. Looked at that way.
It can be abstracted further I supose. The mutation is simply a change in a code. The code is meaningless without the environment to read it. So it all comes down to the interaction of the code and the environment.

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 12 of 344 (36885)
04-13-2003 12:56 AM
Reply to: Message 11 by NosyNed
04-13-2003 12:10 AM


Re: Maybe some are deleterious
Very astute. That's what I've been getting at. I like the way you put it, though.

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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 13 of 344 (36888)
04-13-2003 2:02 AM
Reply to: Message 12 by crashfrog
04-13-2003 12:56 AM


code and environment
Why thank you. And I'm new here.
But seriously, that's only one way to look at it. The "environment" of the cellular machinery that the code must survive in is pretty stringent.
I don't remember the specific ones but I believe there are genes that are common to all of us (right back to bacteria). These control the cellular division and such if I remember correctly. These seem to be very locked in as any changes would break them and therefore be "deleterious". As the environment becomes more stable and more stringent then any change is deleterious. In an environment with lots of variation and lots of change then there is room for more mutations to find value.
Hmmm I'm not sure how much sense that made.

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Coragyps
Member (Idle past 735 days)
Posts: 5553
From: Snyder, Texas, USA
Joined: 11-12-2002


Message 14 of 344 (36894)
04-13-2003 10:37 AM
Reply to: Message 1 by PhospholipidGen
04-12-2003 1:44 AM


Phospholipid, are you Phospho that once was on the Origins Discussion forum? If you are, do you remember our discussion of Hemoglobin C?

This message is a reply to:
 Message 1 by PhospholipidGen, posted 04-12-2003 1:44 AM PhospholipidGen has replied

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Paul
Inactive Member


Message 15 of 344 (36984)
04-14-2003 1:12 PM
Reply to: Message 1 by PhospholipidGen
04-12-2003 1:44 AM


Agreed Phospho. There is tremendous variety in all species and the so-called proofs of evolutionists are what I believe to be mere variations, or minor changes within the same species. Billions of living organisms and fossils have given us absolutely no evidence whatsoever to show the slightest tendency to evolve out of the original kind to which each belongs. Development and normal growth within a species is Not evolution. Improvement or even new varieties within a species is Not evolution either. Science has demonstrated the law of improvement of a species through breeding and cultivation, however the same law has never been able to produce a New species. The TOE must prove Transmutation- that being a change in nature, substance, form, and alteration of essence by a slow and gradual process of mutation from one species to another, and from the lower to the higher. TOE just cannot find a way to do this, or find existing proof that it has happened, and without a change OF species there can be no evolution. Science has shown us that life will interbreed in closly related variations, but it has also shown us that there is an impassable gulf when interbreeding is attempted between different kinds of species. We all know that there can be no evolution without the power of reproduction in living things. Since reproduction is a prior condition to evolution, it Cannot be a product of it. This fact and the logical neccessity for the power of continued reproduction is a significant stumbling block to TOE. The power of reproduction is Not in the embryo, but only in the mature parent. Can an egg produce an egg? No. Can an egg improve upon itself? No. Improvement can only come in and through the mature form. Therefore, if life needs the mature form first, where does that leave us?? Quite a dilema for TOE indeed.
TRUE Science rejects many aspects of TOE and since not one of the many branches of TOE has been proven, let alone the main theory, I believe it to be purely speculative and at this point in time, quite literally a bankrupt philosophy - most definately not a scientific fact.
Until next time :-)
Paul

This message is a reply to:
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Replies to this message:
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