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Author Topic:   Can mutation and selection increase information?
Taq
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Posts: 7282
Joined: 03-06-2009
Member Rating: 3.9


(4)
Message 106 of 222 (816252)
08-01-2017 12:40 PM
Reply to: Message 104 by RAZD
08-01-2017 11:15 AM


Re: random and non-random mutations
RAZD writes:

(B) IIRC, the areas that are not within the "target areas" are still hit by mutations, but these areas also have evolved mechanism/s to protect/conserve critical functions, so you should be talking about areas that are highly conserved by evolved correction mechanisms not having as high a rate of mutations as non-conserved areas, rather than about areas "targeted" for mutations -- there are no "targets."

For those who are interested, I started a thread a while back on these types of mutational hotspots here. The thread focused on one paper by Wright et al. that described hypermutation in an upregulated gene. As it turns out, actively transcribed genes have an increased rate of mutation, probably due to their single stranded state during transcription. Non-transcribed DNA had lower rates of mutation. This would seem to create a situation where genes for critical functions would have a higher rate of mutation than non-critical functions, or even in "junk DNA". Of course, this is E. coli so eukaryotic mutation rates may be a bit different since those mutations occur in the germ line where transcription may be different than in somatic cells.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 104 by RAZD, posted 08-01-2017 11:15 AM RAZD has acknowledged this reply

  
NoNukes
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Posts: 10126
From: Central NC USA
Joined: 08-13-2010
Member Rating: 1.7


(1)
Message 107 of 222 (816253)
08-01-2017 1:56 PM
Reply to: Message 90 by Vlad
07-28-2017 5:16 AM


Re: Can mutation and selection increase information?
Apparently, NoNukes so far didn’t grasp the textbook basics. What did fitness get to do with probabilities of this or that mutation? True Darwinists tend to slip down to Lamarckism – without fail

Apparently, I am discussing biology with someone who cannot read. Mutations are indeed random with respect to fitness. But the actual fitness testing is a function of the environment in which the organisms reproduce and live. The relative survival of phenotypes is not random, but is instead strongly influenced by whether an organism or a population of organisms have the necessary equipment for survival.

Now whether or not your pompous ass agrees with that statement, it is clear that:

1) My statement above is not about Lamarckian inheritance. Nobody is saying that cold weather produces fur, only that animals with fur may have a survival advantage.
2) you don't understand what people here are saying. Perhaps the reason is something other than reading ability or cognitive dissonance, but for now, I am going with those possibilities.


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

I was thinking as long as I have my hands up … they’re not going to shoot me. This is what I’m thinking — they’re not going to shoot me. Wow, was I wrong. -- Charles Kinsey

I never considered a difference of opinion in politics, in religion, in philosophy, as cause for withdrawing from a friend. Thomas Jefferson

Worrying about the "browning of America" is not racism. -- Faith

I hate you all, you hate me -- Faith


This message is a reply to:
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CRR
Member
Posts: 579
From: Australia
Joined: 10-19-2016


Message 108 of 222 (816264)
08-02-2017 3:59 AM
Reply to: Message 104 by RAZD
08-01-2017 11:15 AM


Re: random and non-random mutations
There are two types of mutations.
1. Mutations that occur randomly in time and space; where time is measured by cell divisions and space is the full length of the genome.
2. Mutations that that are not random in space and time;
they occur at cell division in response to an external trigger
they occur preferentially in some parts of the genome rather than uniformly

They will occur together but type 1 will occur at each cell division and type 2 will occur only when the external trigger happens.

The affect on the phenotype of type 1 will be mostly neutral-harmful and rarely beneficial. These are not goal directed in any way.

However type 2 appear to be goal directed in response to the trigger. If they are random in the target areas of the genome their purpose is still to produce an adaption in response to the stimuli. This will still be the case even if the distribution of harmful-neutral-beneficial is identical in proportions to those produced by type 1. However it is also possible that type 2 targets areas that are more likely to produce beneficial mutations. I doubt there is sufficient evidence to rule this possibility out or in.


This message is a reply to:
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Replies to this message:
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Vlad
Junior Member (Idle past 43 days)
Posts: 27
Joined: 06-03-2017


Message 109 of 222 (816269)
08-02-2017 5:27 AM


Non-random genetic changes
Well, Taq still remains unaware of modeling (incl. imaginary experimenting) as of one of the principal methods of science. He/she still do not surmise that changes in genetic 4-character texts (as distinct from these 26-character) propel biological evolution.
Sheer ferity… No wonder, Taq produces nothing beyond the inexhaustible torrent of blah-blah.
Guys, you arduously chew all the same banalities over and don’t see the very essential: long ago, self-learning evolution did away with dependence on (random) mutations. Instead, biological evolution deftly handles targeted genetic changes – for example, see [James Shapiro. Evolution: a View from the 21st Century, 2011] This is the only way for evolution to create incredibly complex living systems.
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JonF
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Posts: 4001
Joined: 06-23-2003
Member Rating: 3.1


Message 110 of 222 (816279)
08-02-2017 8:51 AM
Reply to: Message 108 by CRR
08-02-2017 3:59 AM


Re: random and non-random mutations
However type 2 appear to be goal directed in response to the trigger.

They do not appear to be goal directed. In some circumstances they are a response to environmental stress.

They are random with respect to fitness.

Unless, of course, you have evidence to the contrary.

No?

Didn't think so.


This message is a reply to:
 Message 108 by CRR, posted 08-02-2017 3:59 AM CRR has responded

Replies to this message:
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Taq
Member
Posts: 7282
Joined: 03-06-2009
Member Rating: 3.9


(1)
Message 111 of 222 (816285)
08-02-2017 10:55 AM
Reply to: Message 109 by Vlad
08-02-2017 5:27 AM


Re: Non-random genetic changes
Vlad writes:

Well, Taq still remains unaware of modeling (incl. imaginary experimenting) as of one of the principal methods of science.

I understand it just fine which is why I know that your model is irrelevant to how biology and evolution works.

Sheer ferity… No wonder, Taq produces nothing beyond the inexhaustible torrent of blah-blah.
Guys, you arduously chew all the same banalities over and don’t see the very essential:

You do realize that you just described your own posts, right?

long ago, self-learning evolution did away with dependence on (random) mutations. Instead, biological evolution deftly handles targeted genetic changes – for example, see [James Shapiro. Evolution: a View from the 21st Century, 2011] This is the only way for evolution to create incredibly complex living systems.

The changes that James Shapiro discusses are random mutations with respect to fitness. If you would like to discuss one of his papers, I would be happy to do so.


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Taq
Member
Posts: 7282
Joined: 03-06-2009
Member Rating: 3.9


(1)
Message 112 of 222 (816286)
08-02-2017 10:59 AM
Reply to: Message 108 by CRR
08-02-2017 3:59 AM


Re: random and non-random mutations
CRR writes:

There are two types of mutations.
1. Mutations that occur randomly in time and space; where time is measured by cell divisions and space is the full length of the genome.
2. Mutations that that are not random in space and time;

You forgot a 3rd one.

3. Mutations that are random with respect to fitness.

They will occur together but type 1 will occur at each cell division and type 2 will occur only when the external trigger happens.

Both of those types are random with respect to fitness. Just because a lottery drawing occurs at a set time on a set day does not stop it from being random.

However type 2 appear to be goal directed in response to the trigger.

Poverty triggering people to buy more lottery tickets does not stop the lottery from being random. Hypermutation triggered by environmental conditions increases the random mutation rate. It is still random and not goal oriented. If it were goal oriented then mutations would only occur at specific bases that only produce beneficial changes.


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Vlad
Junior Member (Idle past 43 days)
Posts: 27
Joined: 06-03-2017


Message 113 of 222 (816342)
08-03-2017 5:22 AM


Mutations and fitness
Well, perhaps Taq is going to invent a quite adequate model of spontaneous evolution … sometime… At that, Taq is apparently acquainted with James Shapiro’s book only by hearsay. Actually, Shapiro has proposed the hypothesis of natural genetic engineering (NGE) – fitness or no fitness.
Moreover, there is no such appearance as individual fitness, in the world of sexual reproduction. An asexual bacterium is endowed with the property of fitness, while an individual, even being quite viable, is not, in the world of sex. Only heterosexual (conspecific) pairs are more or less fit – and for good reason. So Taq, as usual, is merely beating the air. A militant ignorance…
Replies to this message:
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Pressie
Member
Posts: 1858
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.1


Message 114 of 222 (816348)
08-03-2017 8:15 AM
Reply to: Message 113 by Vlad
08-03-2017 5:22 AM


Re: Mutations and fitness
Goodness gracious me. You like word salads. I've got no idea what you're trying to say.

I like data, though. Please present your data. Data can be understood in every language on earth.

Edited by Pressie, : No reason given.


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Taq
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Posts: 7282
Joined: 03-06-2009
Member Rating: 3.9


Message 115 of 222 (816358)
08-03-2017 10:43 AM
Reply to: Message 113 by Vlad
08-03-2017 5:22 AM


Re: Mutations and fitness
Vlad writes:

Well, perhaps Taq is going to invent a quite adequate model of spontaneous evolution … sometime…

The models already exist, from the organismal level down to the molecular level. What specific aspects are you curious about?

Actually, Shapiro has proposed the hypothesis of natural genetic engineering (NGE) – fitness or no fitness.

NGE is random mutation with respect to fitness followed by selection. What Shapiro does is focus on beneficial mutations while ignoring the detrimental and neutral mutations that those mechanisms produce.

Moreover, there is no such appearance as individual fitness, in the world of sexual reproduction. An asexual bacterium is endowed with the property of fitness, while an individual, even being quite viable, is not, in the world of sex. Only heterosexual (conspecific) pairs are more or less fit – and for good reason. So Taq, as usual, is merely beating the air. A militant ignorance…

Individuals can be individually fit, such as having different courtship displays (e.g. peacocks).

Edited by Taq, : No reason given.


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Vlad
Junior Member (Idle past 43 days)
Posts: 27
Joined: 06-03-2017


Message 116 of 222 (816410)
08-04-2017 5:22 AM


Fitness and sexual reproduction
Once again, in the world of asexual reproduction, individuals – say, bacteria – are more or less fit. Yet the world of sex is just another pair of shoes: no individual per se is able to reproduce there. Regrettably, only heterosexual (conspecific) pairs are. Wily Mother Nature…
The idea of fitness is all about reproductive success, about producing viable progeny. At that, in the world of sex, progeny are the system effect of a heterosexual pair and, in science, breaking a system effect down by the system’s components is just prohibited. So, we may talk of individual viability while we by no means may reason upon individual fitness. No way.
Some 7-8 decades ago, the founding fathers of the so-called Modern Synthesis had no idea of system properties, system effects, etc. And so they, in good conscience, operated with the anecdotic idea of individual fitness. Let them do. Yet we live in the second decade of XXI century, and reasoning upon the individual fitness, as regards sexual reproduction, appears sheer ferity.
Then once evolutionary theorists acknowledged invalidity of the individual fitness idea, the whole Modern Synthesis construction would collapse like a rickety house of cards. So sad…
Replies to this message:
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Pressie
Member
Posts: 1858
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.1


Message 117 of 222 (816412)
08-04-2017 7:14 AM
Reply to: Message 116 by Vlad
08-04-2017 5:22 AM


Re: Fitness and sexual reproduction
Good Lord, another word salad. Asexual organisms reproduce just fine.
This message is a reply to:
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CRR
Member
Posts: 579
From: Australia
Joined: 10-19-2016


Message 118 of 222 (816413)
08-04-2017 8:04 AM
Reply to: Message 110 by JonF
08-02-2017 8:51 AM


Re: random and non-random mutations
They do not appear to be goal directed. In some circumstances they are a response to environmental stress.

If they occur in response to environmental stress and the increased mutation rate helps the organism to adapt to that stress then possibly it is goal directed. The goal is to adapt to the stress.
It's a reasonable hypothesis based on the observations, and should not be excluded at this stage.

They [mutations] are random with respect to fitness.

So long as you remember that does not mean 50% harmful and 50% beneficial. The vast majority of mutations are detrimental, probably including those that code for the same amino acid. There is some evidence that even where the mutation codes for the same amino acid it can affect other things such as the rate of production.
This message is a reply to:
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Replies to this message:
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herebedragons
Member
Posts: 1417
From: Michigan
Joined: 11-22-2009


Message 119 of 222 (816418)
08-04-2017 9:01 AM
Reply to: Message 118 by CRR
08-04-2017 8:04 AM


Re: random and non-random mutations
If they occur in response to environmental stress and the increased mutation rate helps the organism to adapt to that stress then possibly it is goal directed. The goal is to adapt to the stress.

...

So long as you remember that does not mean 50% harmful and 50% beneficial. The vast majority of mutations are detrimental, probably including those that code for the same amino acid.

Do the regions that experience increased mutational rates during stress change the ratio of detrimental to beneficial mutations? If not, then mutation is still random with respect to fitness.

It's a reasonable hypothesis based on the observations, and should not be excluded at this stage.

That certain regions are prone to higher rates of mutation and that environmental stress can increase mutation rates in target regions is a known and accepted phenomenon. That is not the same as mutations being "goal directed."

There is some evidence that even where the mutation codes for the same amino acid it can affect other things such as the rate of production.

Keep in mind that in order for a mutation to affect fitness, it must affect the organisms ability to reproduce. So while a mutation that codes for the same amino acid may have energetic effects on a bacterium that may slow it's growth rate enough to give it a slight disadvantage compared to others without the mutation, it is unlikely to have a significant effect on larger organism such as humans.

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:
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JonF
Member
Posts: 4001
Joined: 06-23-2003
Member Rating: 3.1


Message 120 of 222 (816425)
08-04-2017 9:41 AM
Reply to: Message 118 by CRR
08-04-2017 8:04 AM


Re: random and non-random mutations
If they occur in response to environmental stress and the increased mutation rate helps the organism to adapt to that stress then possibly it is goal directed.
The goal is to adapt to the stress.

It's possible but the evidence indicates it is not. Got any evidence it's goal directed?

The mutations we see in response to stress are the same as the mutations we see without stress, just more of them. If the organism is lucky one of them might adapt to the stress. The organism has to be very very lucky. Most organisms won't get an adaptational mutation. BUt a slim chance is better than no chance.

It's a reasonable hypothesis based on the observations, and should not be excluded at this stage.

List the observations and explain why the support your claim, please.

The vast majority of mutations are detrimental, probably including those that code for the same amino acid.

The vast majority of mutations are neutral. What evidence do you have "those that code for the same amino acid" are detrimental?

There is some evidence that even where the mutation codes for the same amino acid it can affect other things such as the rate of production.

Evidence please?

And what does that have to do with the fact that responses to stress are random with respect to fitness?


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