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Author Topic:   No genetic bottleneck proves no global flood
AZPaul3
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Posts: 3422
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.8


(1)
Message 121 of 140 (721221)
03-05-2014 9:07 AM
Reply to: Message 119 by Faith
03-05-2014 8:58 AM


Re: Neutral, deleterious or beneficial
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 ...

I already told you.

How does the change affect fitness?

Obviously, the mutation makes no change in fitness. It is called neutral.

That's all there is.

I am not aware of any specific technical name for the concept "mutation that does not change protein" except "neutral."

Sorry, I forgot the second part of your post. Are mutations that do not change proteins the most common type?

Neutral mutations are the most common type.

What percentage of these involve protein changes or not, or happen in non-coding regions or do change phenotype with no affect on fitness, I don't think anyone knows.

Edited by AZPaul3, : No reason given.


This message is a reply to:
 Message 119 by Faith, posted 03-05-2014 8:58 AM Faith has responded

Replies to this message:
 Message 122 by Faith, posted 03-05-2014 9:32 AM AZPaul3 has responded

  
Faith
Member
Posts: 23978
Joined: 10-06-2001
Member Rating: 1.0


Message 122 of 140 (721223)
03-05-2014 9:32 AM
Reply to: Message 121 by AZPaul3
03-05-2014 9:07 AM


Re: Neutral, deleterious or beneficial
I already told you.

How does the change affect fitness?

Obviously, the mutation makes no change in fitness. It is called neutral.

That's all there is.

There is an observed change in the phenotype but no change in fitness, is that what you are saying?

I am not aware of any specific technical name for the concept "mutation that does not change protein" except "neutral."

Which is exactly how I was using the term which caused all this brouhaha for no purpose apparently.

There was another brouhaha not long ago about some other supposed misuse of terminology I was guilty of, I hope it will come back to me, because while reading through some threads I discovered one of your very own using that term in the very same sense I was using it. I meant to post on that, got distracted I guess. I hope I remember it eventually.

Sorry. I forgot the second part of your post. Are mutations that do not change proteins the most common type?

Neutral mutations are the most common type.

What percentage of these involve protein changes or not, or happen in non-coding regions or do change phenotype with no affect on fitness, I don't think anyone knows.

Neutral mutations with respect to fitness then is what you are talking about. But obviously if there is no change in phenotype you are looking at the DNA and calling mutations at that level "neutral" but how can they be "neutral with respect to fitness" if you see no change in the phenotype anyway? So you see mutations at the DNA level and call them "neutral" although you see no change whatever in the phenotype. I'm sorry, I know I'm not getting this question asked clearly, but there's something odd about your statement, like it implies switching back and forth from DNA level observation to phenotypic observation but not making a change in the terminology with respect to fitness. Sorry, I'm tired. If you can make sense of this please answer it but I have to get some sleep.


This message is a reply to:
 Message 121 by AZPaul3, posted 03-05-2014 9:07 AM AZPaul3 has responded

Replies to this message:
 Message 123 by AZPaul3, posted 03-05-2014 9:56 AM Faith has not yet responded
 Message 124 by herebedragons, posted 03-05-2014 11:14 AM Faith has not yet responded

    
AZPaul3
Member
Posts: 3422
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.8


(4)
Message 123 of 140 (721224)
03-05-2014 9:56 AM
Reply to: Message 122 by Faith
03-05-2014 9:32 AM


Re: Neutral, deleterious or beneficial
There is an observed change in the phenotype but no change in fitness, is that what you are saying?

That is one type of neutral mutation, yes. Another is the one you are on about: mutation of an allele without the protein change. (I think JonF has it. Silent Mutation would be a good term for this one.)

I am not aware of any specific technical name for the concept "mutation that does not change protein" except "neutral."

Which is exactly how I was using the term which caused all this brouhaha for no purpose apparently.

But "neutral" mutations involve many other types as well. And your statement that

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 the crux of all this part of the discussion. Recognize that "neutral" refers to affect on fitness regardless of where the mutations occur or what form they take.

But obviously if there is no change in phenotype you are looking at the DNA and calling mutations at that level "neutral" but how can they be "neutral with respect to fitness" if you see no change in the phenotype anyway?

You are right. If the mutation(s) cause no change in phenotype then there cannot be any change in fitness ... sooo ... those mutations are called "neutral".

Faith, it does not matter if the mutation(s) change the allele but not the protein, change the protein but not the phenotype or change the phenotype ... if the mutation does not affect fitness it is termed "neutral". Yes, any mutation that does not change the phenotype can have no affect on fitness. Yes, it falls in the neutral category with all the other mutations that have no affect on fitness.

Edited by AZPaul3, : No reason given.

Edited by AZPaul3, : No reason given.

Edited by AZPaul3, : wow, I'm bad at this today.


This message is a reply to:
 Message 122 by Faith, posted 03-05-2014 9:32 AM Faith has not yet responded

  
herebedragons
Member
Posts: 1251
From: Michigan
Joined: 11-22-2009
Member Rating: 5.6


(2)
Message 124 of 140 (721227)
03-05-2014 11:14 AM
Reply to: Message 122 by Faith
03-05-2014 9:32 AM


Re: Neutral, deleterious or beneficial
I'm sorry, I know I'm not getting this question asked clearly, but there's something odd about your statement, like it implies switching back and forth from DNA level observation to phenotypic observation but not making a change in the terminology with respect to fitness. Sorry, I'm tired. If you can make sense of this please answer it but I have to get some sleep.

They are trying to get across that the terms "neutral, beneficial and deleterious" refer specifically to the effect a mutation has on the organism's fitness, ie. it's ability to reproduce. It does not refer to any particular change in DNA or protein or phenotype, but only the effect on the organism.

However, I would suspect that any mutation that has an effect on phenotype would be either beneficial or deleterious and not neutral. The beneficial or deleterious effect may be so inconsequential so as to call it neutral, but none-the-less I think there would be some effect. But still, neutral doesn't mean that it has no effect on phenotype - it means it has no effect on fitness.

Also keep in mind that phenotype doesn't just mean something you can see, it may also be a biochemical process that you have no idea has changed just by observing the organism.

The other major point is that you really can't use terms like beneficial, deleterious or neutral without context of the environment. Thus a change can be beneficial in one environment and deleterious in another. It's about the context of fitness, how is the organism's ability to reproduce affected?

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 122 by Faith, posted 03-05-2014 9:32 AM Faith has not yet responded

  
herebedragons
Member
Posts: 1251
From: Michigan
Joined: 11-22-2009
Member Rating: 5.6


(1)
Message 125 of 140 (721228)
03-05-2014 11:41 AM
Reply to: Message 119 by Faith
03-05-2014 8:58 AM


Re: Neutral, deleterious or beneficial
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

As Jon pointed out, Silent mutation may be a better term for what you are describing.

But I think what is more confused is that you wouldn't refer to a mutation in an allele unless you were talking about something that changed the function of that allele. Additionally, there are more ways to change function besides changing the protein. What if the mutation was in a promoter region so that the gene produced twice as much gene product, but the protein itself does not change? This could very well be the case in mice having darker fur (I don't know that it is but this is a common situation). Melanin or whatever pigment is in their fur) could be produced at two or three times the rate as in tan mice and produce darker fur. No change in protein - just more of it. Would this be a different allele? Yes, without even changing the protein.

I'd also appreciate very much knowing if I'm correct that this is the most common kind of mutation.

More specifically you are asking about mutations to the gene. Yes, most mutations occur in non-coding regions where they are invisible to selection, ie. neutral.

HBD

Edited by herebedragons, : might not be melanin in the fur - but probably is


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 119 by Faith, posted 03-05-2014 8:58 AM Faith has not yet responded

  
Taq
Member
Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


(2)
Message 126 of 140 (721233)
03-05-2014 12:53 PM
Reply to: Message 105 by Faith
03-04-2014 11:09 PM


Re: Neutral, deleterious or beneficial
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.

Here are the terms that geneticists use.

A silent mutation is a mutation that does not significantly alter the phenotype.

Synonymous mutations are mutations in coding regions that do not alter the amino acid sequence of the protein.

Non-synonymous mutations are mutations that change the amino acid sequence.

Neutral mutations are mutations that do not change the fitness of the organism.

Deleterious mutations lower fitness.

Beneficial mutations increase fitness.

Silent mutations are going to be neutral since not changing the phenotype will not change fitness.

Mutations that do alter phenotype can be neutral, deleterious, or beneficial, depending on how they change fitness in a defined environment. Non-synonymous mutations can be silent or not silent. Non-synonymous mutations that are not silent can be neutral, deleterious, or beneficial.

To simplify this a bit, there are three stages of questions. First, does a mutation occur in a position that could change phenotype, that is does it occur in functional DNA and change gene expression or function. Second, does it change phenotype. Third, does it change fitness.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 105 by Faith, posted 03-04-2014 11:09 PM Faith has not yet responded

  
Taq
Member
Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


(1)
Message 127 of 140 (721237)
03-05-2014 1:14 PM
Reply to: Message 116 by Faith
03-05-2014 8:42 AM


Re: Neutral, deleterious or beneficial
I've understood that this sort of change that does not change the protein is the MOST COMMON kind of mutation too.

Being the most common is not the same as being the only type of mutation.


This message is a reply to:
 Message 116 by Faith, posted 03-05-2014 8:42 AM Faith has not yet responded

  
CreationPigeon
Junior Member (Idle past 902 days)
Posts: 2
Joined: 07-06-2014


Message 128 of 140 (732473)
07-07-2014 6:41 PM


I believe this problem could be solved with my theory about the flood.

Aquatic life, insects, amphibians and small, semi-aquatic animals such as otters and monitor lizards would not need to be on the ark as they could survive either in the flood waters or on floating vegetation mats. As reasonably large populations of these would have survived, there is no visible bottleneck. Evolutionists have criticized this, saying that the mix of salt and fresh water would kill off most life, but the fact that the original animal kinds were more resistant to change than today's animal species and the fact that the fresh flood waters would float on top of the saltwater oceans refutes this.

As for the ark animals, there is a bottleneck. Evolutionists have discovered an allegedly 70,000 year-old one in humans, chimpanzees. orangutans, macaques, cheetahs, tigers and gorillas (look for "Toba catastrophe theory"). More genetic research will probably reveal more. The micro-evolution of the original animal kinds and diversification of the human race that occurred after the flood probably caused scientists to think the bottleneck was 70,000 years old, rather than 4,300 years old.


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hooah212002
Member (Idle past 256 days)
Posts: 3180
Joined: 08-12-2009


Message 129 of 140 (732474)
07-07-2014 6:52 PM
Reply to: Message 128 by CreationPigeon
07-07-2014 6:41 PM


So a flood that covered the entire earth in a matter of days was so calm as to allow lizards to ride on mats in sufficient numbers to not have a genetic bottleneck? Have you ever seen a flood before?

As reasonably large populations of these would have survived

Going to need some data here. Math is sufficient, I guess. Be sure to look up at which section of the forum you are in. Since you are here, in the science department, you need to bring some evidence for your wild ass claims.

but the fact that the original animal kinds were more resistant to change than today's animal species

Says who? Says what evidence? Dinosaurs sure didn't seem to like change too much, else they'd still be here. Nor did mammoths or sabre cats.

Evolutionists have discovered an allegedly 70,000 year-old one in humans, chimpanzees. orangutans, macaques, cheetahs, tigers and gorillas

So because some other event potentially caused a genetic bottleneck, how does that do anything for a flood idea (notably NOT a "theory")?

The micro-evolution of the original animal kinds and diversification of the human race that occurred after the flood probably caused scientists to think the bottleneck was 70,000 years old, rather than 4,300 years old.

Ah, the famed "super fast evolution" that seemed to happen after the "flood" for which there is zero evidence. Or do you claim that you know how to date fossils and strata better than people that spent their entire lives doing just that?

Oh, welcome to EvC. Enjoy the stay and if someone leaves a cookie on your pillow, I suggest not eating it.


Organic life is nothing but a genetic mutation, an accident. Your lives are measured in years and decades. You wither and die. We are eternal, the pinnacle of evolution and existence. Before us, you are nothing. Your extinction is inevitable. We are the end of everything.

This message is a reply to:
 Message 128 by CreationPigeon, posted 07-07-2014 6:41 PM CreationPigeon has not yet responded

    
herebedragons
Member
Posts: 1251
From: Michigan
Joined: 11-22-2009
Member Rating: 5.6


Message 130 of 140 (732476)
07-07-2014 7:11 PM
Reply to: Message 128 by CreationPigeon
07-07-2014 6:41 PM


Hi, and welcome CreationPigeon

Aquatic life, insects, amphibians and small, semi-aquatic animals such as otters and monitor lizards would not need to be on the ark as they could survive either in the flood waters or on floating vegetation mats.

First problem is that the Bible says that all living creatures were killed by the flood except those that were on the ark. Now, one could argue what "alive" means.
Gen 6:7 says

quote:
I will blot out man whom I have created from the face of the land, from man to animals to creeping things and to birds of the sky;

Gen 7:21 - 23 says:
quote:
All flesh that moved on the earth perished, birds and cattle and beasts and every swarming thing that swarms upon the earth, and all mankind; of all that was on the dry land, all in whose nostrils was the breath of the spirit of life, died. Thus He blotted out every living thing that was upon the face of the land, from man to animals to creeping things and to birds of the sky, and they were blotted out from the earth; and only Noah was left, together with those that were with him in the ark.

So maybe plants, fish and insets are not included in this list, but its hard to justify that "amphibians and small, semi-aquatic animals such as otters and monitor lizards " were not destroyed by the flood.

Second problem depends on what kind of flood it was. Some YECs believe that the flood was so catastrophic that it stripped the land bare and laid all that sediment back down in layers miles thick. It is kind of hard to imagine that anything, fish, plants, insects - anything, could survive such a catastrophic event.

Now if you imagine a gentle, semi-lethal event, well then it may be possible for some creatures that weren't listed as being killed to survive. However, now we will have trouble explaining geological features in a YEC time frame.

HBD

Note: use the peek button at the bottom of the frame to see how quote boxes are formatted. For other formatting issues you can click on dBCodes

Edited by herebedragons, : No reason given.


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 128 by CreationPigeon, posted 07-07-2014 6:41 PM CreationPigeon has not yet responded

Replies to this message:
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Faith
Member
Posts: 23978
Joined: 10-06-2001
Member Rating: 1.0


Message 131 of 140 (732477)
07-07-2014 7:27 PM
Reply to: Message 128 by CreationPigeon
07-07-2014 6:41 PM


But if you're talking only about the smaller animals there wouldn't be any reason for them to be left off the ark as there would be plenty of room for them. And I think the bottleneck applies even to the sea creatures that were left in the ocean. Not all died but likely most of them. Me, I'd look for the percentage of junk DNA in a creature's genome as a clue to whether it went through the Flood bottleneck or not, thinking of junk DNA as a record of death in a species: the more junk DNA the less the creature was affected by the bottleneck.
This message is a reply to:
 Message 128 by CreationPigeon, posted 07-07-2014 6:41 PM CreationPigeon has not yet responded

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Faith
Member
Posts: 23978
Joined: 10-06-2001
Member Rating: 1.0


Message 132 of 140 (732479)
07-07-2014 7:33 PM
Reply to: Message 130 by herebedragons
07-07-2014 7:11 PM


Really the Bible doesn't say all "living" creatures but those on "the face of the land," leaving the sea creatures in the ocean, which were killed in great numbers (I judge by the fossil record) but not totally wiped out. And then, as you point out, the list of creatures also leaves out sea creatures and plants.

Also, the scenario you are describing as that of YECs is pretty much my own. I don't know if it reflects other YECs or not, or to what extent. It's simply a way to explain where the sediments came from that formed the strata, and it makes sense, based on the idea of forty days and nights of rain, that pretty much everything that could be dissolved or turned into mud would have been.

Edited by Faith, : No reason given.


This message is a reply to:
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herebedragons
Member
Posts: 1251
From: Michigan
Joined: 11-22-2009
Member Rating: 5.6


Message 133 of 140 (732486)
07-07-2014 8:44 PM
Reply to: Message 132 by Faith
07-07-2014 7:33 PM


I meant to say "some YECs" rather than "So ..." Anyway, it is not an uncommon argument the YECs use, that the flood laid down the strata and deposited the fossil record. I don't think I have heard anyone but you actually say that the material for the geological column came from scouring the land, but it is the only "logical" place it could have come from.

So, how could sea creatures have survived a catastrophe of the magnitude you imagine?

HBD

Edited by Adminnemooseus, : Off-topic banner.


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 132 by Faith, posted 07-07-2014 7:33 PM Faith has not yet responded

  
Adminnemooseus
Director
Posts: 3740
Joined: 09-26-2002


Message 134 of 140 (732489)
07-07-2014 9:06 PM


LET'S KEEP THIS TOPIC ON-TOPIC
All messages should have something directly connection to the term "genetic bottleneck"

We already have a catch-all flood geology topic happening at Continuation of Flood Discussion

Adminnemooseus

Edited by Adminnemooseus, : Toggle ID.


Or something like that.

    
NoNukes
Member
Posts: 9330
From: Central NC USA
Joined: 08-13-2010
Member Rating: 2.6


Message 135 of 140 (732492)
07-07-2014 10:19 PM
Reply to: Message 132 by Faith
07-07-2014 7:33 PM


Pick your poetry...
ally the Bible doesn't say all "living" creatures but those on "the face of the land,"

That's a pretty extreme job of cherry picking. The Bible describes who got the axe during the flood in various ways.

From the King James Version.

quote:
17 I am going to bring floodwaters on the earth to destroy all life under the heavens, every creature that has the breath of life in it. Everything on earth will perish.

Even if you translate earth as land, something I would have no issue with, the rest of 6:17 certainly covers a lot more ground that just land animals, with "All life under the heavens" being pretty the most inclusive phrase.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

I have never met a man so ignorant that I couldn't learn something from him. Galileo Galilei

If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass


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