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Author Topic:   Are mutations truly random or are they guided?
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 61 of 134 (548778)
03-01-2010 6:49 PM
Reply to: Message 53 by slevesque
03-01-2010 4:40 PM


Re: Neutral mutations
First, doesn't this destroy Kimura's theory of molecular evolution (since it relies on the fact that the vast majority of mutations are nearly-neutral) ?
Firstly, slightly beneficial mutations are also near-neutral; secondly, neutral mutations are actually neutral. Slightly deleterious mutations are a proper subset of those which have little or no effect.
Also, please bear in mind that Kimura doesn't rely on the mutations being near neutral rather than completely neutral. Rather, Kimura's theory can cope with near-neutral mutations. The closer they are to neutral, the more their long-term fate will be decided by drift rather than selection, so for sufficiently near-neutral mutations, selection can be overlooked for the sake of doing the math.
(By analogy, I think you said you do physics. Remember how for the sake of the math, when analyzing the motion of a pendulum, you can take sin xx when x is small? It's like that.)
There are more deleterious mutations then beneficial ...
But are there significantly more slightly deleterious mutations than slightly beneficial ones?
... and even with a very favorable ratio of 3:1
I don't see how this estimate (unsupported, I note, by facts) is generous. Surely after all this time we must be very close to the equilibrium point at which the fixation of deleterious mutations by drift is balanced by the fixation of beneficial mutations by drift and selection?
Edited by Dr Adequate, : No reason given.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 62 of 134 (548779)
03-01-2010 6:52 PM
Reply to: Message 59 by slevesque
03-01-2010 6:36 PM


Re: Neutral mutations
many mutations are so subtle that it doesn't have any noticeable effect on the phenotype.
That you cannot discern the minute difference does not mean it is not there. In another environment it may have a profound effect on survival and reproducibility. I would guess lots of mutations are nothing more that some unique fold in one small corner of a protein. Unnoticed, benign. Until ...
Edited by AZPaul3, : No reason given.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 63 of 134 (548781)
03-01-2010 7:04 PM
Reply to: Message 59 by slevesque
03-01-2010 6:36 PM


Re: Neutral mutations
A nearly-neutral mutations by it's very definition is one who has no perceivable effect by NS. This includes selective pressures in any environment.
(emphasis mine)
I understand Natural selection.
No, you do not.
Edited by AZPaul3, : No reason given.

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


Message 64 of 134 (548783)
03-01-2010 7:27 PM
Reply to: Message 53 by slevesque
03-01-2010 4:40 PM


Re: Neutral mutations
This would mean that of all the mutations I have from my parents, only 10% are slightly deleterious and the rest are detectable by selection ?
Obviously it doesn't mean this at all, for the reasons that Dr. A went into, some of those mutations will be genuinely neutral and some may be slightly beneficial, others will have larger effects on fitness and will be suitable targets for selection.
As to how natural selection will ever sort them, once again you are following the same song sheet as Smooth Operator in the other thread. Has no one in the ID/Creationist camp ever looked into basic genetics? Things like genetic recombination and the effects of sexual reproduction? That is how nature sorts them out, random assortment allowing the segregation of few or many deleterious mutations to one chromosome, and at a higher level amongst genomes, where they may be more prone to selection due to the cumulative or combinatorial effects of the deleterious mutations (Keightley and Otto, 2006).
TTFN,
WK

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 65 of 134 (548786)
03-01-2010 8:21 PM
Reply to: Message 28 by Percy
03-01-2010 9:18 AM


unreal expectations based on false information
Hi Percy,
Given that we don't know everything and never will, there will always be questions for which we have few or no answers. Concerning examples of positive mutations in mammals, I'd be surprised if we know of very many.
Note that Bolder-dash is not concerned with real mutations at all. What he wants is evidence of single point mutations that form whole new features.
Message 24: Neither you, nor anyone else, can give any examples of positive random mutations cropping up spontaneously in animal populations, such that would develop into new, functioning systems or organs.
In other words the "hopeful monster" mutation misrepresentation used by those ignorant of real evolution.
(ibid): For a theory that depends ENTIRELY on a continuation of these type of developments happening in every animal population, your non-existence of actual examples of them is remarkable to say the least.
And ignorant of what the theory of evolution is really about. We saw this ignorance firmly adhered to in the previous threads, and a complete refusal to learn about reality, so I don't expect any real progress in understanding to be evidenced. Good luck.
Enjoy.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 66 of 134 (548868)
03-02-2010 7:52 AM
Reply to: Message 44 by Wounded King
03-01-2010 3:19 PM


Wounded King writes:
A neutral mutation is more like if you changed the way the code was typed but not its functionality, for a bash example it is like changing ' if test $i -ge 10' into 'if [ $i -ge 10 ]'.
And assuming that neutral mutations can happen to unexpressed regions of DNA, that would be like changing "# This is a comment" into "# This is still a comment".
A bash analogy? Are you sure you're a biologist?
--Percy

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Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 67 of 134 (548873)
03-02-2010 8:33 AM
Reply to: Message 56 by slevesque
03-01-2010 4:45 PM


Re: Neutral mutations
slevesque writes:
A nearly-neutral mutations by it's very definition is one who has no perceivable effect by NS. This includes selective pressures in any environment.
I read forward and found you're yet unconvinced, so let me add my voice to the others: a neutral mutation in one environment is definitely not neutral in all other environments.
The reason a mutation is neutral is important. If neutral because it is completely unexpressed, for example a point mutation that doesn't affect the gene at all and the gene continues to produce the same protein as before, then that kind of mutation should be neutral in all environments.
But if neutral because the change it produces has no effect on reproductive success, then the neutrality is definitely specific to that environment. In other environments the change may not be neutral. For example, say a mutation changes a beetle's carapace color from brown to musky red, and in the current environment that turns out to be neutral. Then one day the local ecology is invaded by a beetle predator that can see musky red better than it can see brown. Guess what, the mutation isn't neutral any more.
--Percy

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Bolder-dash
Member (Idle past 3630 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 68 of 134 (548876)
03-02-2010 8:45 AM
Reply to: Message 65 by RAZD
03-01-2010 8:21 PM


Re: unreal expectations based on false information
This is a good expalantion for why your side gets beat up so bad in live debates (see Meyer/Sternberg vs. Shermer/Prothero).
You have little to say to defend your own theory, and rely on the tired old saw of claiming a monopoly on knowledge, and go read a biology book. Man what a bore your (Taz, Dr. A, Percy, ad infinitum...) answers are.
It is YOUR side that says these random mutations are so numerous as to be able to explain the existence of all of life's complexities-yet you can show none.
You make the erroneous claim, over and over btw, that I am seeking some magical point mutation of a completed new system. Absolutely not; but since your side claims all of these complex systems start with some mutation-a mutation big enough to cause a reproductive advantage-surely you should at least be able to show a few starting points right? There are billions and billions of them happening all the time your side claims (how else could we get billions and billions of completed complexities?), so show a few happening in modern times. What does the starting point look like? A shriveled ear? An indented forehead? Where does a new body part begin?
Percy of course tried to squirm out this dilemma by mentioning bacteria, but even then he couldn't give any examples of anything. The fact is that when you talk about bacteria your sides argument gets even weaker-we have witnessed in our lifetimes billions and billions of generations of bacteria-and not a single new complex system has seen to have been formed-nothing leading down the path of greater complex organisms. If you can't show it in billions of generations-how many is it going to take to just get ONE? There isn't enough time in all of history times 10 to make even one very very simple new system for life, if we go by the rate at which bacteria changes!
So, the only hopeful monster in the room seems to be your theory, claiming for all its worth, a divine exclusivity on the facts-while providing no evidence whatsoever. You say its random mutations, you say random mutations can give advantages over other individuals, enough to cause a building of a great pyramid-well you are simply being asked to show some of this. Instead your side can only attack the doubters-instead of fortifying your own argument. That is why your side loses debates, and why your side requires all the blind faith you claim in others.
Edited by Bolder-dash, : Blinded by the audacity of your empty claims, I somehow missed a parentheses.

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Replies to this message:
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 Message 85 by Dr Adequate, posted 03-02-2010 4:05 PM Bolder-dash has replied
 Message 86 by RAZD, posted 03-02-2010 6:52 PM Bolder-dash has replied
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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 69 of 134 (548887)
03-02-2010 9:41 AM
Reply to: Message 62 by AZPaul3
03-01-2010 6:52 PM


Re: Neutral mutations
I would guess lots of mutations are nothing more that some unique fold in one small corner of a protein.
IIRC, only about 3 mutations out of 125 to 175 mutations per person occur in a coding region. Of the rest I don't see how even a majority of them will change gene expression. I think it would be a safe bet that most mutations do not affect either gene expression or amino acid sequence in any noticeable way.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 70 of 134 (548888)
03-02-2010 9:48 AM
Reply to: Message 68 by Bolder-dash
03-02-2010 8:45 AM


Re: unreal expectations based on false information
Absolutely not; but since your side claims all of these complex systems start with some mutation-a mutation big enough to cause a reproductive advantage-surely you should at least be able to show a few starting points right? There are billions and billions of them happening all the time your side claims (how else could we get billions and billions of completed complexities?), so show a few happening in modern times. What does the starting point look like? A shriveled ear? An indented forehead? Where does a new body part begin?
Take any two species. Compare their genomes. Homologous bases are the beginning points. Differences are the mutations.
The fact is that when you talk about bacteria your sides argument gets even weaker-we have witnessed in our lifetimes billions and billions of generations of bacteria-and not a single new complex system has seen to have been formed-nothing leading down the path of greater complex organisms.
Strawman. Evolution is not change from simple to complex. It is adaptation. Bacteria have been evolving for over 3 billion years to fill their niche. That niche requires simplicity. To this day the most successful path is simplicity. Even now the vast majority of life is single celled. Why should bacteria become more complex when simplicity has served them so well for over 3 billion years?
There isn't enough time in all of history times 10 to make even one very very simple new system for life, if we go by the rate at which bacteria changes!
Where is your math? It has already been shown that the observed human mutation rate is consistent with the change needed to produce the differences between humans and chimps.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 71 of 134 (548890)
03-02-2010 9:58 AM
Reply to: Message 40 by Species8472
03-01-2010 2:44 PM


I have a question for you guys. I'm an engineering student doubling with computer science. With programing, I have a bad habit of commenting out whole sections of codes, sometimes even whole subroutines, instead of deleting them when I don't use them. I also have the bad habit of reusing programs time after time after adjusting them just a little to do their purpose. The result after a while are programs with hundreds of lines of codes that's been commented out. Sometimes, I even leave things running if they absolutely not affect the result I wanted.
Am I to understand that "neutral" mutations are somewhat like these junk codes?
It works as a rough analogy. To extend the analogy, imagine if you were using an old floppy drive to copy files from one computer to the next. It just so happens that a few mistakes are made each time the file is copied leading to changes in the code. Changes that occur in the commented sections will go unnoticed while changes in the areas required for the program will either create bugs or perhaps change the program for the better.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 72 of 134 (548892)
03-02-2010 10:09 AM
Reply to: Message 69 by Taq
03-02-2010 9:41 AM


Re: Neutral mutations
I think it would be a safe bet that most mutations do not affect either gene expression or amino acid sequence in any noticeable way.
I can agree with this.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 73 of 134 (548893)
03-02-2010 10:09 AM
Reply to: Message 39 by slevesque
03-01-2010 2:11 PM


I'll add another point that hasn't been highlighted. If the cell had a mechanism to provoke the mutations it needed, that would help it along it's evolution (asI understood the OP) then this very same mechanism would have had to have evolved. and since it wasn't there to direct it's own happening, classical evolution with random mutation are what made this mechanism in the first place.
What is actually happening with such mechanisms as the SOS response in E. coli is it increases the random mutation rate by upregulating sloppy polymerases and increases the recombination rates in areas where the DNA has been damaged. What the bacteria are doing (if you want to anthropomorphize it) is trading an increase in deleterious mutations for the chance of hitting that one mutation that will allow it to survive in harsh conditions.
The problem with a specific mutations in response to specific stimuli is that competitors who randomly mutate will outsmart them. For example, let's look at the competition between bacteria and antibiotic producing fungi. Let's say that the bacteria can sense penicillin in the environment and in response produce a specific mutation that results in a B-lactamase enzyme that cleaves the penicillin. What happens when the fungus randomly mutates and produces a derivative of penicillin that is still bactericidal but is no longer recongnized by the B-lacatamase produced by the bacteria? The bacteria are gonners.
I don't doubt that life COULD have a set mutational response to specific environmental cues. However, such a system would be quickly outpaced randomly mutating competitors.
Edited by Taq, : No reason given.

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Bolder-dash
Member (Idle past 3630 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 74 of 134 (548895)
03-02-2010 10:22 AM
Reply to: Message 70 by Taq
03-02-2010 9:48 AM


Re: unreal expectations based on false information
Strawman. Evolution is not change from simple to complex. It is adaptation. Bacteria have been evolving for over 3 billion years to fill their niche.
Strawman. Your side is claiming is HAS evolved from simple to complex. So what has happened to bacteria. In a trillion billion generations it has gone from bacteria to.... bacteria?
How many more chances do you think your side should get? You claim it takes time...I don't know how much longer we can wait.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 75 of 134 (548896)
03-02-2010 10:25 AM
Reply to: Message 74 by Bolder-dash
03-02-2010 10:22 AM


Re: unreal expectations based on false information
Strawman. Your side is claiming is HAS evolved from simple to complex.
Our side is arguing that only a few lineages have gone from simple to complex. The vast majority of lineages started simple and remain simple. On top of that, evolution does not require simple to complex, only less fit to more fit in a given environment.
Bacteria have been evolving for over 3 billion years to fill niches open to simple organisms. Why would you expect a couple of months of selection to reverse this trend?

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