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Author Topic:   How novel features evolve #2
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 127 of 402 (671315)
08-24-2012 10:38 AM
Reply to: Message 4 by RAZD
05-23-2012 10:44 AM


Re: DNA sequences and Phenotype selection
...I would suggest that the cause (random or designed) of a mutation...
Why do you ignore the third (and more propable after epigenetics and the recent immence flow of knowledge about RNA) possibility, that of information from environment causing guided mutations?
Edited by zi ko, : No reason given.

This message is a reply to:
 Message 4 by RAZD, posted 05-23-2012 10:44 AM RAZD has seen this message but not replied

Replies to this message:
 Message 128 by New Cat's Eye, posted 08-24-2012 11:30 AM zi ko has replied
 Message 129 by Taq, posted 08-24-2012 11:46 AM zi ko has replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 130 of 402 (671436)
08-25-2012 12:55 AM
Reply to: Message 128 by New Cat's Eye
08-24-2012 11:30 AM


Re: DNA sequences and Phenotype selection
The evnironment doesn't reach the genome in order to mutate it.
-------------------------------------------------------------------------------You seem so sure.... Can you bring any evidenc for random mutations in metazoa?


This message is a reply to:
 Message 128 by New Cat's Eye, posted 08-24-2012 11:30 AM New Cat's Eye has replied

Replies to this message:
 Message 132 by New Cat's Eye, posted 08-27-2012 10:20 AM zi ko has replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 131 of 402 (671439)
08-25-2012 1:40 AM
Reply to: Message 129 by Taq
08-24-2012 11:46 AM


Re: Is there any evidence of random mutation?
We ignore it because the evidence doesn't support it.
So what is the evidence supporting creationism or, most importanly, random mutations in metazoa?
On another thread on the same question you gave me this.
I quote:
Abstract
"I estimate per nucleotide rates of spontaneous mutations of different kinds in humans directly from the data on per locus mutation rates and on sequences of de novo nonsense nucleotide substitutions, deletions, insertions, and complex events at eight loci causing autosomal dominant diseases and 12 loci causing X-linked diseases. The results are in good agreement with indirect estimates, obtained by comparison of orthologous human and chimpanzee pseudogenes. The average direct estimate of the combined rate of all mutations is 1.8x10(-8) per nucleotide per generation, and the coefficient of variation of this rate across the 20 loci is 0.53. Single nucleotide substitutions are approximately 25 times more common than all other mutations, deletions are approximately three times more common than insertions, complex mutations are very rare, and CpG context increases substitution rates by an order of magnitude. There is only a moderate tendency for loci with high per locus mutation rates to also have higher per nucleotide substitution rates, and per nucleotide rates of deletions and insertions are statistically independent on the per locus mutation rate. Rates of different kinds of mutations are strongly correlated across loci. Mutational hot spots with per nucleotide rates above 5x10(-7) make only a minor contribution to human mutation. In the next decade, direct measurements will produce a rather precise, quantitative description of human spontaneous mutation at the DNA level."
Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases - PubMed
------------------------------------------------------------------------------and my answer was:
I Quote:
"So this famed evidence about random mutations in metazoa ends up to an indirect estimation by a scientist, who in 2002, hopes that other scientists, during next decade (which already had ended), would rather make a direct measurement, evidently necessary for any conclusion!!!!"
Have you since foumd a better evidence tha this?
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 129 by Taq, posted 08-24-2012 11:46 AM Taq has replied

Replies to this message:
 Message 133 by Taq, posted 08-27-2012 1:49 PM zi ko has replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 134 of 402 (671611)
08-28-2012 12:32 PM
Reply to: Message 133 by Taq
08-27-2012 1:49 PM


Re: Meaningless controvercy.
So why would cells guide the process of mutation to produce these diseases? Or are mutations random, producing a wide range of effects?
Guided mutations does not mean strictly determined mutations. In the theory of environment-genes interrelation, there is always place for relative randomness in mutations.
It seems the gap between the evollution theories is closing rapidly. It had proved beyond any doupt that stress causes genes mutations.So the mechanism for it exists in metazoa. Randomness and environmental information are useful to natural life, so are used equally well by nature, most propably radomness more often in monocells, while in metazoa, where neural system is developed guidance is more propable.


This message is a reply to:
 Message 133 by Taq, posted 08-27-2012 1:49 PM Taq has replied

Replies to this message:
 Message 135 by Taq, posted 08-28-2012 12:42 PM zi ko has replied
 Message 136 by New Cat's Eye, posted 08-28-2012 1:18 PM zi ko has not replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 137 of 402 (671906)
08-31-2012 11:06 AM
Reply to: Message 132 by New Cat's Eye
08-27-2012 10:20 AM


Re: DNA sequences and Phenotype selection
The article you suggested is very interesting.
I quote from it:
"Although most mutations are believed to be caused by replication errors, they can also be caused by various environmentally induced and spontaneous changes to DNA that occur prior to replication but are perpetuated in the same way as unfixed replication errors. As with replication errors, most environmentally induced DNA damage is repaired, resulting in fewer than 1 out of every 1,000 chemically induced lesions actually becoming permanent mutations. The same is true of so-called spontaneous mutations. "Spontaneous" refers to the fact that the changes occur in the absence of chemical, radiation, or other environmental damage. Rather, they are usually caused by normal chemical reactions that go on in cells, such as hydrolysis. These types of errors include depurination, which occurs when the bond connecting a purine to its deoxyribose sugar is broken by a molecule of water, resulting in a purine-free nucleotide that can't act as a template during DNA replication, and deamination, which results in the loss of an amino group from a nucleotide, again by reaction with water. Again, most of these spontaneous errors are corrected by DNA repair processes. But if this does not occur, a nucleotide that is added to the newly synthesized strand can become a permanent mutation."
So environment causes gene mutations! I can add stress as an environmental factor causing gene mutations.
But i think there is a serious omission on this work. There isn't any relation as to if the error repairing actions are directed to special types of mutations, leaving others to perpatuate.
In that case we would have a serious evidence or not of guided mutations.
Edited by zi ko, : No reason given.
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 132 by New Cat's Eye, posted 08-27-2012 10:20 AM New Cat's Eye has replied

Replies to this message:
 Message 139 by New Cat's Eye, posted 08-31-2012 11:23 AM zi ko has not replied
 Message 140 by Percy, posted 08-31-2012 11:26 AM zi ko has replied
 Message 145 by Taq, posted 08-31-2012 12:53 PM zi ko has replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 138 of 402 (671908)
08-31-2012 11:14 AM
Reply to: Message 135 by Taq
08-28-2012 12:42 PM


Re: Meaningless controvercy.
I see a lot of vague claims but zero evidence.
--------------------------------------------------------------------------------
Read please my message 137 to Catholic Scientist.
Edited by zi ko, : No reason given.


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 Message 135 by Taq, posted 08-28-2012 12:42 PM Taq has not replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 147 of 402 (672107)
09-03-2012 10:19 AM
Reply to: Message 140 by Percy
08-31-2012 11:26 AM


Re:meaningless controvercy
What has this to do with how novel features evolve?
If cells are directing repairing mechanisms only to some specific DNA damage and not all, then there is surely a matter of guided evolution. That is what i meant saying that this work suffered a serious ommission.
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 140 by Percy, posted 08-31-2012 11:26 AM Percy has replied

Replies to this message:
 Message 148 by Percy, posted 09-03-2012 10:39 AM zi ko has not replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 149 of 402 (672112)
09-03-2012 11:09 AM
Reply to: Message 143 by Percy
08-31-2012 12:04 PM


Re: Meaningless controvercy.
I think the current understanding is that environmentally caused mutations can matter a great deal
It was a great step forward, don't you think?
Anyway accepting increased rate mutation, caused by environment is not far away from accepting guided evolution! (note: not mutation). Random mutations is a usefull mechanism not to be used by nature, in its scope to evolution, specifically in mono cell organisms. But here we reach at the main issue, the core problem we have to face: Are natural laws enough to explain life emergence and next evolution? Or we have to resort to the Supernatural?
Edited by zi ko, : No reason given.
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 143 by Percy, posted 08-31-2012 12:04 PM Percy has replied

Replies to this message:
 Message 151 by Percy, posted 09-03-2012 12:02 PM zi ko has replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 150 of 402 (672114)
09-03-2012 11:25 AM
Reply to: Message 145 by Taq
08-31-2012 12:53 PM


Re: Meaningless controvercy.
Yes, and those mutations are random with respect to fitness. We are all aware that chemical mutagens and radiation cause mutations. We are also aware of things like the SOS response in E. coli. In each case, the mutations that are produced are random with respect to fitness.
I have no dificulty to accept all that, with the presuppposition we had solved firstly the core question: Are natural laws enough to explain life appearance and concequently species evolution ?
In the case of positive answer we accept that natural laws are guiding evolution (not mutations!). In the other case Supernatural is doing it.
In either case it is secondary, at least philosofically, if there are only random mutations, or only guided mutations, or both of them.
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 145 by Taq, posted 08-31-2012 12:53 PM Taq has replied

Replies to this message:
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zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 152 of 402 (672142)
09-04-2012 12:57 AM
Reply to: Message 128 by New Cat's Eye
08-24-2012 11:30 AM


Re:choosing the easy enemy?
The evnironment doesn't reach the genome in order to mutate it.
Can isuppose,after Percy's intervention, you agree that it is not so?


This message is a reply to:
 Message 128 by New Cat's Eye, posted 08-24-2012 11:30 AM New Cat's Eye has replied

Replies to this message:
 Message 155 by New Cat's Eye, posted 09-04-2012 9:51 AM zi ko has not replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 153 of 402 (672144)
09-04-2012 2:02 AM
Reply to: Message 151 by Percy
09-03-2012 12:02 PM


Re: choosing the propper opponent?
Percy,
Only few messages before ( 127) i have posed a question ) clearly inside the topic),which i recieved no clear answer yet, though it relates to the central question of biology.Your hastiness to close the issue, seems to me rather curious...


This message is a reply to:
 Message 151 by Percy, posted 09-03-2012 12:02 PM Percy has replied

Replies to this message:
 Message 154 by Percy, posted 09-04-2012 7:13 AM zi ko has not replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 164 of 402 (672258)
09-05-2012 9:16 AM
Reply to: Message 140 by Percy
08-31-2012 11:26 AM


Re: DNA sequences and Phenotype selection
There has never been any doubt in anyone's mind that both the environment and stress ......... can cause mutations, but these mutations are random with respect to fitness.
Can you clarify please if about similar environmental changes cause about similar or not mutations on other members of the species?


This message is a reply to:
 Message 140 by Percy, posted 08-31-2012 11:26 AM Percy has replied

Replies to this message:
 Message 165 by Percy, posted 09-05-2012 9:30 AM zi ko has not replied

  
zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 166 of 402 (672264)
09-05-2012 9:53 AM
Reply to: Message 159 by Percy
09-04-2012 12:44 PM


Re: choosing the propper opponent?
What if creationists are pathologically incapable of posting on-topic? Or is it a skill you worked on? A strategy you're purposefully employing? An odd mental quirk? Maybe we could discuss this question too in every thread, along with guided evolution and philosophical questions about the nature of evidence. Why have forums and threads, anyway? Why not just go to a single thread with a few hundred thousand messages?
What if evolutionists avoid (for what reason?) answering crucial questions and use authority to get away? Of course i am off topic now , but you were the same just before me.When i posed a simple question on message 127, i just got an authoritarian NO, based on such a meagre evidence and against any contemporary scientific knowledge.


This message is a reply to:
 Message 159 by Percy, posted 09-04-2012 12:44 PM Percy has seen this message but not replied

Replies to this message:
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zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 173 of 402 (672335)
09-07-2012 12:34 AM
Reply to: Message 171 by Percy
09-06-2012 2:26 PM


Re: Topic warning
It seemed like Zi Ko was trying to co-opt yet another thread to discuss his own favorite ideas,
It isn't so bad after all, if it is not off topic. You just fight and redicule , if you can, my ideas. Choosing "proper" opponents it is not scientific at least.
Edited by zi ko, : No reason given.

This message is a reply to:
 Message 171 by Percy, posted 09-06-2012 2:26 PM Percy has replied

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zi ko
Member (Idle past 3645 days)
Posts: 578
Joined: 01-18-2011


Message 175 of 402 (672356)
09-07-2012 10:09 AM
Reply to: Message 170 by Taq
09-06-2012 11:23 AM


Re: Topic warning
This offers a way of testing whether mutations are guided or random with respect to fitness. Given the multitude of possible mutations in different genes that can give rise to dark fur we would not expect random mutations to result in the same mutation in independent populations. If mutations are guided then we would expect the same mutations to occur in each population. What do we observe? Different mutations in each populaton. This is extremely strong evidence for random mutations.
We can apply this same knowledge to evolution in general. Given the random nature of mutations and the contigencies within the genomes that they occur in we would expect different solutions to the same problem in different lineages. This is why we see feathers and fur as two separate solutions for thermoregulation in mammals and birds. This is why we see different solutions for eyes, wings, and fins amongst different lineages.
I would easily agree, if we accept guidance as the act of an omnipotent all knowing Supernatural choosing the best, in our opinion, procedure. But this is not the case.
According to my thesis guidance is expressed by the information flow from environment to genome. It is not strictly determined. It is a loosely directed try and error process. In one cell organisms even pure randomness can be allowed for, if is economical, as nature can use all available means in its scope to preserve and evolve life. Maybe this is the procedure Supernatural had chosen to act . Maybe it is just a matter of natural laws . So your deductions do not seem so strong, as other mechanisms could have as well the same results.
As for the need of evidence I say:
After about 250 ys what is the evidence for random mutations in metazoa? Almost negligible, understandably though. Because of complexity of the subject (see discussion of pocket mouse issue) it is difficult to expect proofs. But the fact is remaining. Your laboratory examples are based on one cell organisms, not on metazoa.
How would we then expect clear cut evidence for guided evolution in order to just discuss the issue?
Still , accepting lately the importance of environmental effect on genome sequence is quite enough to justifiably discussing it in this thread .
We know of spontaneous mutations. Do we know for sure that these are not the result o some kind of environmental pressure?
Stress in chicken causes always the same behavior disturbances. Isn’t it an indication of guided genome change, due environmental pressure? The same I think applies to pocket mouse coloring.
Can we say with confidence that the repairing mechanism is not guided, so to ensure the perpetuation of useful mutations? Of course I should have brought the evidence in favor of my case, not just ask questions. I think we share the same fate. You don’t have it either. Can we agree on that?
Edited by zi ko, : No reason given.

This message is a reply to:
 Message 170 by Taq, posted 09-06-2012 11:23 AM Taq has replied

Replies to this message:
 Message 176 by Taq, posted 09-07-2012 1:00 PM zi ko has replied
 Message 179 by RAZD, posted 09-09-2012 12:55 PM zi ko has replied

  
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