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Author Topic:   No genetic bottleneck proves no global flood
Tanypteryx
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Posts: 1556
From: Oregon, USA
Joined: 08-27-2006
Member Rating: 5.2


(1)
Message 106 of 140 (721199)
03-04-2014 11:23 PM
Reply to: Message 105 by Faith
03-04-2014 11:09 PM


Re: Neutral, deleterious or beneficial
A neutral mutation is one that doesn't change what the allele would have done anyway

That is not the only meaning of "neutral mutation". It can also cause a change in the phenotype that in the present environment is not positively or negatively selected. It is neutral as far as selection is concerned.


What if Eleanor Roosevelt had wings? -- Monty Python

One important characteristic of a theory is that is has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie

If evolution is shown to be false, it will be at the hands of things that are true, not made up. --percy


This message is a reply to:
 Message 105 by Faith, posted 03-04-2014 11:09 PM Faith has responded

Replies to this message:
 Message 107 by Faith, posted 03-04-2014 11:53 PM Tanypteryx has responded

    
Faith
Member
Posts: 25848
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 107 of 140 (721202)
03-04-2014 11:53 PM
Reply to: Message 106 by Tanypteryx
03-04-2014 11:23 PM


Re: Neutral, deleterious or beneficial
I have not heard it used that way, and in any case in this discussion it's only being used in the sense I gave it. It confuses the issues to give it another meaning. The point I was making was that a neutral mutation would not produce an allele for dark fur in a light colored population, and most of the mutations are neutral in that sense, as I've learned from the experts here and on the internet. So let's not change the definition midstream.
This message is a reply to:
 Message 106 by Tanypteryx, posted 03-04-2014 11:23 PM Tanypteryx has responded

Replies to this message:
 Message 108 by Tanypteryx, posted 03-05-2014 2:44 AM Faith has responded

    
Tanypteryx
Member
Posts: 1556
From: Oregon, USA
Joined: 08-27-2006
Member Rating: 5.2


(3)
Message 108 of 140 (721208)
03-05-2014 2:44 AM
Reply to: Message 107 by Faith
03-04-2014 11:53 PM


Re: Neutral, deleterious or beneficial
So let's not change the definition midstream.

I'm not changing the definition. I'm saying that your definition is incomplete and in fact is misleading.

When biologists talk about neutral mutations we mean that they are neutral to selection, not that they don't change anything. Sometime they don't change anything, but sometimes they do and it doesn't affect selection.

The point I was making was that a neutral mutation would not produce an allele for dark fur in a light colored population

I am not saying that dark fur in a light population is neutral because it is bloody obvious that in the mouse populations we are talking about the light and dark mutations can be either beneficial or deleterious depending on which of the two habitats they occur in.

The whole point of this discussion is about selection, so when we say neutral, deleterious or beneficial it seems obvious that we mean in terms of selection.

I think your understanding is incorrect or at least incomplete and that is making hard for you to understand what you are being told.


What if Eleanor Roosevelt had wings? -- Monty Python

One important characteristic of a theory is that is has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie

If evolution is shown to be false, it will be at the hands of things that are true, not made up. --percy


This message is a reply to:
 Message 107 by Faith, posted 03-04-2014 11:53 PM Faith has responded

Replies to this message:
 Message 109 by Faith, posted 03-05-2014 5:17 AM Tanypteryx has not yet responded

    
Faith
Member
Posts: 25848
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 109 of 140 (721209)
03-05-2014 5:17 AM
Reply to: Message 108 by Tanypteryx
03-05-2014 2:44 AM


Re: Neutral, deleterious or beneficial
You can't just decide what the words mean after I've been using them in another sense. You even acknowledged I'm using it correctly but now you want to insist on another meaning I'm not using.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 108 by Tanypteryx, posted 03-05-2014 2:44 AM Tanypteryx has not yet responded

Replies to this message:
 Message 110 by vimesey, posted 03-05-2014 7:02 AM Faith has responded
 Message 112 by AZPaul3, posted 03-05-2014 7:32 AM Faith has responded

    
vimesey
Member
Posts: 888
From: Birmingham, England
Joined: 09-21-2011
Member Rating: 4.0


(1)
Message 110 of 140 (721210)
03-05-2014 7:02 AM
Reply to: Message 109 by Faith
03-05-2014 5:17 AM


Re: Neutral, deleterious or beneficial
Of course you can.

Words can have different meanings in different contexts. Take "proof". In mathematics, it refers to a demonstration, absolutely and without any other possibility, that a mathematical proposition is correct - it's an on/off switch - something is absolute or not - there are no nuances.

In criminal law, (in my country at least), it means proof beyond reasonable doubt. And in civil law, it means proof on the balance of probabilities. So it's very nuanced in law.

Different contexts, different meanings.

So if you change context, and the common usage of a word in that context is different from the usage in a previous context, you need to change your meaning. Tan isn't deciding what words mean - as an expert in the field, Tan is telling you how the word is used in the relevant context. I grant you, it's a slight pain, but it's the way it is.


Could there be any greater conceit, than for someone to believe that the universe has to be simple enough for them to be able to understand it ?

This message is a reply to:
 Message 109 by Faith, posted 03-05-2014 5:17 AM Faith has responded

Replies to this message:
 Message 111 by Faith, posted 03-05-2014 7:15 AM vimesey has not yet responded

    
Faith
Member
Posts: 25848
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 111 of 140 (721211)
03-05-2014 7:15 AM
Reply to: Message 110 by vimesey
03-05-2014 7:02 AM


Re: Neutral, deleterious or beneficial
The point is that I was using the word in a particular sense, which Tanypteryx agreed was correct in itself, so that of course one CAN come along and totally miss my point by using it in another sense but that would only serve to muddle things. If that is your aim, then of course go right ahead and create the great muddle you desire. I'll just go away, which is perhaps the whole point anyway.
This message is a reply to:
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AZPaul3
Member
Posts: 3428
From: Phoenix
Joined: 11-06-2006


(4)
Message 112 of 140 (721212)
03-05-2014 7:32 AM
Reply to: Message 109 by Faith
03-05-2014 5:17 AM


Re: Neutral, deleterious or beneficial
You can't just decide what the words mean ...

That is correct, in this specific context, you cannot. Mutations have always been deleterious, beneficial or neutral with respect to fitness.

That means that any phenotypic trait that results from the mutations hinders, enhances or has no effect on the individuals ability to survive and reproduce in a specific environment.

The fur-color example is classic. The same mutations (darker fur) are deleterious in one environment (lighter ground) and beneficial in another (lava field). The mutations affect that individual's fitness in that specific environment.

This changes your point that:

quote:
... a neutral mutation would not produce an allele for dark fur in a light colored population, and most of the mutations are neutral in that sense ...

Neutral mutations would not alter fitness. But if we assume (in the matter under discussion) that darker fur in a lighter environment detracts from fitness then darker fur in a lighter environment is always termed deleterious and can never be considered neutral. It has too great an effect, and a direct effect, on the individual's fitness. So you are right. Neutral mutations would not make dark fur in a light environment, but not for the reasons you think.

Your idea from message 105:

quote:
A neutral mutation is one that doesn't change what the allele would have done anyway. It's not related to the level of selection.

... is terribly wrong and needs to change.

All mutations are always defined by their effects on the individual's fitness (read "selection"). The result of the mutations may very well change the resultant protein coded by that allele (change its function), and may well change some attribute of the phenotype. But if the phenotype differences do not affect the individual's fitness then the mutations that under lay that change are termed "neutral". And, furthermore, this assessment of the same mutations effects on fitness may very well change with a change in environment.

[emphasis]

In defining mutations as deleterious, beneficial or neutral it does not matter how the allele function is altered. The only thing that matters is the resulting fitness of the individual.

[/emphasis]

This is how deleterious, beneficial and neutral mutations have always been defined in every discussion, in every book and on every site. Throughout all the discussions on this board these definitions with respect to fitness have always been the meanings of those words. If you have been using some other idea of what those words mean then you have been very wrong. Nosey and Tany are correct.

You need to rethink your stance with respect to the actual definitions of these words and bring your discussions in line with the accepted meanings everyone else in the entire world has been using for decades.

Edited by AZPaul3, : No reason given.

Edited by AZPaul3, : No reason given.

Edited by AZPaul3, : No reason given.

Edited by AZPaul3, : hoo boy. I'll never get this right!


This message is a reply to:
 Message 109 by Faith, posted 03-05-2014 5:17 AM Faith has responded

Replies to this message:
 Message 114 by Faith, posted 03-05-2014 8:03 AM AZPaul3 has responded

  
PaulK
Member
Posts: 12969
Joined: 01-10-2003
Member Rating: 3.2


(2)
Message 113 of 140 (721213)
03-05-2014 7:37 AM
Reply to: Message 111 by Faith
03-05-2014 7:15 AM


Re: Neutral, deleterious or beneficial
Since you said:


Well, this is what I've gleaned from many online presumably science-based discussions of the information. THEY say this, I get it from THEM. The vast majority are neutral, many others are deleterious

it would follow that the relevant meaning would be the one used by "THEM", which would be the standard definition, not your idea of what "THEY" meant. It seems that in reality you are the one trying to change meanings by changing definitions.


This message is a reply to:
 Message 111 by Faith, posted 03-05-2014 7:15 AM Faith has not yet responded

    
Faith
Member
Posts: 25848
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 114 of 140 (721214)
03-05-2014 8:03 AM
Reply to: Message 112 by AZPaul3
03-05-2014 7:32 AM


Re: Neutral, deleterious or beneficial
So there is always a change in the phenotype as a result of ANY mutation? That is certainly not what I've understood from many an encounter with the concepts, but if that is the case then I stand corrected.

ABE That is the only point that has mattered in how I've used the term.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 112 by AZPaul3, posted 03-05-2014 7:32 AM AZPaul3 has responded

Replies to this message:
 Message 115 by AZPaul3, posted 03-05-2014 8:13 AM Faith has responded

    
AZPaul3
Member
Posts: 3428
From: Phoenix
Joined: 11-06-2006


(2)
Message 115 of 140 (721215)
03-05-2014 8:13 AM
Reply to: Message 114 by Faith
03-05-2014 8:03 AM


Re: Neutral, deleterious or beneficial
So there is always a change in the phenotype as a result of ANY mutation?

Where did this come from? I never said that.

There can be code changes in an allele that do not change the protein being produced. In that case the mutations can not alter the phenotype.

That is the only point that has mattered in how I've used the term.

Then, in a deep technical sense, you are still wrong. The mutation is labeled "neutral" not because the protein did not change but because the change did not affect the individual's fitness.

Edited by AZPaul3, : No reason given.


This message is a reply to:
 Message 114 by Faith, posted 03-05-2014 8:03 AM Faith has responded

Replies to this message:
 Message 116 by Faith, posted 03-05-2014 8:42 AM AZPaul3 has responded

  
Faith
Member
Posts: 25848
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 116 of 140 (721216)
03-05-2014 8:42 AM
Reply to: Message 115 by AZPaul3
03-05-2014 8:13 AM


Re: Neutral, deleterious or beneficial
There can be code changes in an allele that do not change the protein being produced. In that case the mutations can not alter the phenotype.

That is the only thing I've been using the term for. So if the term for that is not "neutral mutation" give me a term for it.

I've understood that this sort of change that does not change the protein is the MOST COMMON kind of mutation too.

If that is also not correct, then please give me the correct information.


This message is a reply to:
 Message 115 by AZPaul3, posted 03-05-2014 8:13 AM AZPaul3 has responded

Replies to this message:
 Message 117 by JonF, posted 03-05-2014 8:48 AM Faith has not yet responded
 Message 118 by AZPaul3, posted 03-05-2014 8:51 AM Faith has responded
 Message 127 by Taq, posted 03-05-2014 1:14 PM Faith has not yet responded

    
JonF
Member
Posts: 3881
Joined: 06-23-2003
Member Rating: 3.3


(2)
Message 117 of 140 (721217)
03-05-2014 8:48 AM
Reply to: Message 116 by Faith
03-05-2014 8:42 AM


Re: Neutral, deleterious or beneficial
Silent mutation is closer than "Neutral mutation". There might be other terms I don't know.
This message is a reply to:
 Message 116 by Faith, posted 03-05-2014 8:42 AM Faith has not yet responded

  
AZPaul3
Member
Posts: 3428
From: Phoenix
Joined: 11-06-2006


(3)
Message 118 of 140 (721218)
03-05-2014 8:51 AM
Reply to: Message 116 by Faith
03-05-2014 8:42 AM


Re: Neutral, deleterious or beneficial
You are missing the point.

The point is not whether a protein is changed or not or what you call it if it does or doesn't.

The point is only what effect the change has on fitness.

Pick a change, any change. Does it affect fitness up, down or sideways in some specified environment?

There then you have beneficial, deleterious and neutral.

Do not add anything else to the mix.

Edited by AZPaul3, : added environment.


This message is a reply to:
 Message 116 by Faith, posted 03-05-2014 8:42 AM Faith has responded

Replies to this message:
 Message 119 by Faith, posted 03-05-2014 8:58 AM AZPaul3 has responded

  
Faith
Member
Posts: 25848
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 119 of 140 (721219)
03-05-2014 8:58 AM
Reply to: Message 118 by AZPaul3
03-05-2014 8:51 AM


Re: Neutral, deleterious or beneficial
But I am not addressing the level of fitness, I'm interested in what the mutation actually does to the allele, and that's the only thing I've been discussing. So I'm not missing the point though I may have the terminology wrong. Again, I'd like to know what term I could use for the mutation in an allele that does not change the protein it codes for, and I'd also appreciate very much knowing if I'm correct that this is the most common kind of mutation.
This message is a reply to:
 Message 118 by AZPaul3, posted 03-05-2014 8:51 AM AZPaul3 has responded

Replies to this message:
 Message 121 by AZPaul3, posted 03-05-2014 9:07 AM Faith has responded
 Message 125 by herebedragons, posted 03-05-2014 11:41 AM Faith has not yet responded

    
RAZD
Member
Posts: 18858
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.6


(1)
Message 120 of 140 (721220)
03-05-2014 9:06 AM
Reply to: Message 105 by Faith
03-04-2014 11:09 PM


Neutral, deleterious or beneficial -- to selection pressure
No, Nosy, that is not how the terms are used. A neutral mutation is one that doesn't change what the allele would have done anyway. It's not related to the level of selection.

False. That IS how the terms are used.

Whether any change is neutral, deleterious or beneficial is entirely determined by how it affects the relative survival and reproductive ability of the individual in the current ecology. Change the ecology and the relative results may shift.

A black mouse in a tan ecology with hungry hawks is deleterious, especially compared to tan mice.

A tan mouse in a black ecology with hungry hawks is deleterious, especially compared to black mice.

Classic natural selection.


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This message is a reply to:
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