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Author Topic:   Random mutations
Sylas
Member (Idle past 3680 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 16 of 35 (209556)
05-19-2005 1:33 AM
Reply to: Message 15 by Limbo
05-19-2005 1:22 AM


Not stopping, but slowing.
Limbo writes:

Are mutations as random as we thought? Maybe mutations are controlled by pre-programming. If so, how could we have evolved the program in the first place?

This is quite counter to the actual ideas explored in the cited article. They are proposing that there is a protein which helps modulate the rate at which mutation occurs. In conditions of stress, the mutation rate can increase.

There is no suggestion that the mutations are controlled in the sense of affecting the result of mutations. Only the rate is affected. The mutations remain as random as ever.

Hence it is not about "stopping" evolution. It is about "slowing" evolution. There will always be a background mutation rate. If there is an accelerator protein, however, then perhaps its effect can be blocked so that bacteria are not quite as "mutable", and will take rather longer to become resistant to antibiotics.

Cheers -- Sylas

This message has been edited by Sylas, 05-19-2005 01:38 AM


This message is a reply to:
 Message 15 by Limbo, posted 05-19-2005 1:22 AM Limbo has responded

Replies to this message:
 Message 17 by Limbo, posted 05-19-2005 1:45 AM Sylas has responded

  
Limbo
Inactive Member


Message 17 of 35 (209560)
05-19-2005 1:45 AM
Reply to: Message 16 by Sylas
05-19-2005 1:33 AM


Re: Not stopping, but slowing.
quote:
There will always be a background mutation rate.

Could you elaborate on this a little? I'm trying to figure out how this could happen in the first place.

I mean, life would have to arise with the slowest possible mutation rate as a default rate, right? And it would have to evolve ways of initiating mutations in their own DNA...very very slowly, right? And it would have to evolve them without initiating them on its own, right? Wouldnt that take millions or even billions of years?

It seems to me, as a mere member of the public, that its like waiting for a computer operating system to evolve on a blank hard-drive.

This message has been edited by Limbo, 05-19-2005 01:48 AM


This message is a reply to:
 Message 16 by Sylas, posted 05-19-2005 1:33 AM Sylas has responded

Replies to this message:
 Message 18 by Wounded King, posted 05-19-2005 2:08 AM Limbo has responded
 Message 20 by Sylas, posted 05-19-2005 2:23 AM Limbo has responded

  
Wounded King
Member (Idle past 2515 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 18 of 35 (209564)
05-19-2005 2:08 AM
Reply to: Message 17 by Limbo
05-19-2005 1:45 AM


Re: Not stopping, but slowing.
I think part of the problem is that the article is somewhat misleading.

This brought Romesberg to the conclusion that mutation is a programmed stress response -- a survival mechanism.

This has to be an over generalisation. The mechanism of many induced and spontaneous mutations is already well established and there is no reason to assume that mutations which arise by these means need any specific 'evolved' mutational systems, for instance de-amination converting methyl-cytosine to thymine.

I mean, life would have to arise with the slowest possible mutation rate as a default rate, right?

No reason why it should. There are a number of proteins whose job it is to maintain accurate copies of genetic material since the processes of DNA replication are inherently proen to error. Why pre-suppose some ancestral perfect system of replication, especially since such a system would, as you note, effectively preclude evolution from occurring.

It would only be true if mutation had to evolve, if mutation is a natural process mediated both by environmental factors and the mechanisms of genetic replication, then there is no problem with a continuously present rate of background mutation.

That fact that evolving a mutator phenotype is good for bacteria doesn't mean that all mutation is due to evolved systems.

TTFN,

WK


This message is a reply to:
 Message 17 by Limbo, posted 05-19-2005 1:45 AM Limbo has responded

Replies to this message:
 Message 19 by Limbo, posted 05-19-2005 2:18 AM Wounded King has responded

  
Limbo
Inactive Member


Message 19 of 35 (209565)
05-19-2005 2:18 AM
Reply to: Message 18 by Wounded King
05-19-2005 2:08 AM


Re: Not stopping, but slowing.
quote:
There are a number of proteins whose job it is to maintain accurate copies of genetic material since the processes of DNA replication are inherently proen to error.

I guess what Im getting at is this: these proteins whose job it is to maintain accurate copies of genetic material would have to slowly evolve through spontaneous mutations without the aid of any self-initiated mechanisms? Because the very mechanisms life uses to evolve arent there yet.

It just seems as if the first organism wouldnt even have the basic tools it needs to even evolve in the first place.


This message is a reply to:
 Message 18 by Wounded King, posted 05-19-2005 2:08 AM Wounded King has responded

Replies to this message:
 Message 21 by Wounded King, posted 05-19-2005 2:49 AM Limbo has responded

  
Sylas
Member (Idle past 3680 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 20 of 35 (209566)
05-19-2005 2:23 AM
Reply to: Message 17 by Limbo
05-19-2005 1:45 AM


Re: Not stopping, but slowing.
Limbo writes:

I mean, life would have to arise with the slowest possible mutation rate as a default rate, right?

No, in fact.

Generally speaking, mutation is a bad thing. But chemistry being what it is, replication is never perfect, and this is why there is always a small background mutation rate.

If, perchance, something changes to make the replication a bit more stable, that will tend to persist. So over time, the fidelity or accuracy of mutation has tended to increase. In Eukaryotic organisms, for example, some quite complicated cellular machinery has developed to repair errors that creep into DNA replication. The accuracy achieved by DNA replication is quite astounding. It seems that only about one error for every 100000000 bases copied is the going rate. Without the evolved repair mechanisms, there would be more errors.

Since a human genome has about 6000000000 bases, we have roughly 60 or so mutations occurring with each replication of cell. These numbers are a bit off and not known to full accuracy, but basically we all carry a significant number of new mutation introduced since our parents. The situation is complicated by the fact that there are hot spots where mutation is more common, and cold spots where it is less common. Repair slows replication, which carries a cost. So repair tends to be focused on important parts of the genome.... I think.

In any case, the very first replicators probably had high mutation rates, and over time evolution helped bring these down. A major problem for origin of life ideas is how to get an earlier replicator of sufficient accuracy that it is not overwhelmed by mutation loads.

But under stress... that is, an organism finding itself in an environment for which it is not well adapted... there may be a benefit to having a slight increase in mutation rates.

Cheers -- Sylas


This message is a reply to:
 Message 17 by Limbo, posted 05-19-2005 1:45 AM Limbo has responded

Replies to this message:
 Message 22 by Limbo, posted 05-19-2005 3:06 AM Sylas has responded

  
Wounded King
Member (Idle past 2515 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 21 of 35 (209569)
05-19-2005 2:49 AM
Reply to: Message 19 by Limbo
05-19-2005 2:18 AM


Re: Not stopping, but slowing.
It just seems as if the first organism wouldnt even have the basic tools it needs to even evolve in the first place.

But errors in replication are the fundamental tool needed to evolve. As long as you have a system which imperfectly replicates with heritable traits you should see some form of natural selection working to favour those traits which improve replication frequency.

There is obviously a trade off between levels of mutation high enough to facilitate the occurrence of mutations with potentially beneficial phenotypes and levels so high that they destroy beneficial phenotypes. The fact that there are cellular systems for both error cheching and for inducing mutation show that evolution has acted to fine tune this balance to an acceptable level while still maintaining the potential for increased mutation in stressful environments.

In pre-cellular life the most beneficial trait is simply going to be that of increasing the rate of , at least relatively true, replication.

Simply by virtue of the way selection works those traits which allow both lots of replication and the maintenance of traits promoting replication are bound to be favoured.

Because the very mechanisms life uses to evolve arent there yet.

Many of those mechanisms are there as they are based on inherent chemical properties of genetic material. Certain mechanisms, such as the mutator system in that paper, will not be there, but mutation will still occur.

TTFN,

WK


This message is a reply to:
 Message 19 by Limbo, posted 05-19-2005 2:18 AM Limbo has responded

Replies to this message:
 Message 23 by Limbo, posted 05-19-2005 3:20 AM Wounded King has responded
 Message 25 by Cold Foreign Object, posted 05-23-2005 8:46 PM Wounded King has responded
 Message 34 by randman, posted 12-23-2005 12:37 AM Wounded King has responded

  
Limbo
Inactive Member


Message 22 of 35 (209570)
05-19-2005 3:06 AM
Reply to: Message 20 by Sylas
05-19-2005 2:23 AM


Re: Not stopping, but slowing.
Thank you Sylvas, Im learning a lot.

quote:
If, perchance, something changes to make the replication a bit more stable, that will tend to persist. So over time, the fidelity or accuracy of mutation has tended to increase.

Couple of basic questions. This process you decribe would have happened in the 'primordial soup', correct? Is it technically chemical evolution or organic evolution? Are we talking about the kind of organism created in the Miller-Urey experiment? Does natural selection play a role in selecting beneficial mutation at this point?

quote:
But under stress... that is, an organism finding itself in an environment for which it is not well adapted... there may be a benefit to having a slight increase in mutation rates.

Is this where natural selection kicks in? The organism which can speed up mutation survives to reproduce?


This message is a reply to:
 Message 20 by Sylas, posted 05-19-2005 2:23 AM Sylas has responded

Replies to this message:
 Message 26 by Sylas, posted 05-23-2005 10:14 PM Limbo has not yet responded

  
Limbo
Inactive Member


Message 23 of 35 (209573)
05-19-2005 3:20 AM
Reply to: Message 21 by Wounded King
05-19-2005 2:49 AM


Re: Not stopping, but slowing.
quote:
Many of those mechanisms are there as they are based on inherent chemical properties of genetic material.

Im just wondering where that genetic material came from in the first place. It had to have come from inorganic chemical responces, right?

quote:
As long as you have a system[...]

By system do you mean DNA? Does the mechanism give rise to the system, or does the system give rise to the mechanism? Where does Miller-Urey tie in to all this?

This message has been edited by Limbo, 05-19-2005 03:20 AM

This message has been edited by Limbo, 05-19-2005 03:45 AM


This message is a reply to:
 Message 21 by Wounded King, posted 05-19-2005 2:49 AM Wounded King has responded

Replies to this message:
 Message 24 by Wounded King, posted 05-19-2005 7:01 AM Limbo has not yet responded

  
Wounded King
Member (Idle past 2515 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 24 of 35 (209611)
05-19-2005 7:01 AM
Reply to: Message 23 by Limbo
05-19-2005 3:20 AM


Re: Not stopping, but slowing.
Im just wondering where that genetic material came from in the first place. It had to have come from inorganic chemical responces, right?

Yes, it would have to have its origin from chemical reactions among components we would not consider to be alive. DNA and RNA can be chemically synthesised, but the processes as we use them are unlikely to bear much relation to their evolutionary origins.

By system do you mean DNA? Does the mechanism give rise to the system, or does the system give rise to the mechanism?

No, I don't neccessarily mean DNA. DNA is what most of the life we are familiar with happens to use at the present time, but there are compelling reasons to think that it was not the original form of replicating genetic information. Self-replicating RNAs would be another example or alternatively PNAs (Nelson, et al., 2000). The mechanisms would in many case already be there as they are simply chemical reactions affecting genetic material, they would be distinct from the mechanisms which initially synthesis that genetic material however in many cases. In the case of errors inherent in the replication of the genetic material they obviously would not have operated before self replicating material was available.

Nelson, et al. 2000 writes:

Numerous problems exist with the current thinking of RNA as the first genetic material. No plausible prebiotic processes have yet been demonstrated to produce the nucleosides or nucleotides or for efficient two-way nonenzymatic replication. Peptide nucleic acid (PNA) is a promising precursor to RNA, consisting of N-(2-aminoethyl)glycine (AEG) and the adenine, uracil, guanine, and cytosine-N-acetic acids. However, PNA has not yet been demonstrated to be prebiotic. We show here that AEG is produced directly in electric discharge reactions from CH4, N2, NH3, and H2O. Electric discharges also produce ethylenediamine, as do NH4CN polymerizations. AEG is produced from the robust Strecker synthesis with ethylenediamine. The NH4CN polymerization in the presence of glycine leads to the adenine and guanine-N9-acetic acids, and the cytosine and uracil-N1-acetic acids are produced in high yield from the reaction of cyanoacetaldehyde with hydantoic acid, rather than urea. Preliminary experiments suggest that AEG may polymerize rapidly at 100°C to give the polypeptide backbone of PNA. The ease of synthesis of the components of PNA and possibility of polymerization of AEG reinforce the possibility that PNA may have been the first genetic material.

So there is a plausible route for the synthesis of PNAs from pre-biotic chemicals. There is also considerable evidence that peptides and related forms, such as PNA or peptoids (Ghosh and Chmielewski, 2004).

Ghosh and Chmielewski, 2004 writes:

The ability to self-replicate utilizing amide-bond synthesis will certainly not be limited to canonical peptides synthesized from a-amino acids, but will be inclusive of most amide-bond-containing heteropolymers capable of
self-assembly. Three new heteropolymers containing amide bonds — PNAs, peptoids and b-peptides — fulfil the self-assembly criteria.

Limbo writes:

Where does Miller-Urey tie in to all this?

Nowhere really, Miller-Urey was the first proof of principle experiment showing the ability of particular elements important for life as we know it, in that case amino acids, from pre-biotic conditions. Given that the atmosphere used in M-U is no longer considered likely for he primitive Earth it is not directly relevant to the history of life on Earth, but it stil stands as a proof of concept.

TTFN,

WK


This message is a reply to:
 Message 23 by Limbo, posted 05-19-2005 3:20 AM Limbo has not yet responded

  
Cold Foreign Object 
Suspended Member (Idle past 1468 days)
Posts: 3417
Joined: 11-21-2003


Message 25 of 35 (210745)
05-23-2005 8:46 PM
Reply to: Message 21 by Wounded King
05-19-2005 2:49 AM


Re: Not stopping, but slowing.
But errors in replication are the fundamental tool needed to evolve.

Errors are tools ?

Of course you are not using "tool" to mean its understood definition.

WK:

Isn't the age of the Earth really based upon the time needed for all the "errors" to produce what is seen today ? Of course you have no evidence of RM outside of logic asserting it must of happened or how else did everything get here.

As long as you have a system which imperfectly replicates with heritable traits you should see some form of natural selection working to favour those traits which improve replication frequency.

How does NS know to improve if it is not intelligent ?

Isn't NS simply the naturalist god ?

Isn't NS simply a euphemism for God ?

Ray Martinez


This message is a reply to:
 Message 21 by Wounded King, posted 05-19-2005 2:49 AM Wounded King has responded

Replies to this message:
 Message 27 by MangyTiger, posted 05-23-2005 10:35 PM Cold Foreign Object has not yet responded
 Message 29 by Wounded King, posted 05-24-2005 4:38 AM Cold Foreign Object has not yet responded

  
Sylas
Member (Idle past 3680 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 26 of 35 (210757)
05-23-2005 10:14 PM
Reply to: Message 22 by Limbo
05-19-2005 3:06 AM


Re: Not stopping, but slowing.
Is this where natural selection kicks in? The organism which can speed up mutation survives to reproduce?

Yes.

There is a rather amusing analogy here with how some bacteria can swim towards light. Some bacteria have flagella that can beat in two different modes. In one mode, the bacterium tends to move in a straight line. In the other mode, the bacterium tends to "tumble" in place.

The bacterium alternates between these two modes, tumbling, and then moving in some direction, then tumbling again, and so on. The direction of movement after tumbling appears to be completely random. How then do they manage to swim towards the light?

Basically, the length of time between tumbles increases when the light level is low.

This means that in low light levels, each straightline movement is longer, and moves it further. In high light levels, the straightline movements are quite short. In either case, the movement is a random walk, but when it is dark the walk tends to cover longer distances, which increases the chance of moving out from the dark regions. When it is in the light, it tends to remain in that vicinity. If it happens to move deeper into darkness; tough. They played the odds and lost.

In an analogous fashion, a bacterium in a stressful environment may replicate with less accuracy, leading to larger "steps" within the genome space. Essentially, it is not where it wants to be, and plays the odds in the "hope" that its daughter bacteria end up into a better position.

None of this is thought out by a bacterium. The chemistry in both cases can be studied. It is complex organic chemistry, but no additional control is applied other than normal chemistry. The selection for changes in the chemistry controlling replication, or flagellum beating, will tend to mean that the survivors in each generation are those that took larger steps in bad circumstances.

Cheers -- Sylas


This message is a reply to:
 Message 22 by Limbo, posted 05-19-2005 3:06 AM Limbo has not yet responded

  
MangyTiger
Member (Idle past 4774 days)
Posts: 989
From: Leicester, UK
Joined: 07-30-2004


Message 27 of 35 (210758)
05-23-2005 10:35 PM
Reply to: Message 25 by Cold Foreign Object
05-23-2005 8:46 PM


What does improved mean ?
Wicked King says in Message 21:

As long as you have a system which imperfectly replicates with heritable traits you should see some form of natural selection working to favour those traits which improve replication frequency.

Ray says in Message 25:

How does NS know to improve if it is not intelligent ?

Hopefully Wounded King won't mind an amateur butting in... and when I get it wrong he'll correct me :)

NS doesn't know and it doesn't need to know. All that needs to happen is the results of replication (the children if you want to think of it in anthropomorphic terms) survive and replicate better than their peers.

In an evolutionary sense "improve" does not mean bigger, stronger, quicker or anything like that. In the post you replied to WK was talking to Limbo about the first organism, but it doesn't matter if it is the very first thing we would regard as alive, a dinosaur or a human today - the concept is still the same.

In evolutionary terms the definition of "improved" or "fitter" is that your offspring do better than your peers offspring because of some trait they inherited.

In simple terms the outcome of Natural Selection is your children live long enough to have more babies than their peers.


Oops! Wrong Planet

This message is a reply to:
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Limbo
Inactive Member


Message 28 of 35 (210776)
05-24-2005 1:12 AM


As we know evolution is a 'blind' process. Could the discovery of “preprogrammed” mechanisms of variation be interpreted as evidence for ID?

What is the relationship between the estimated length of time required for the evolutionary process and the estimated age of the earth? Would “preprogrammed” mechanisms force us to re-evalute the age of the earth?


Replies to this message:
 Message 30 by Wounded King, posted 05-24-2005 4:58 AM Limbo has not yet responded

  
Wounded King
Member (Idle past 2515 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 29 of 35 (210789)
05-24-2005 4:38 AM
Reply to: Message 25 by Cold Foreign Object
05-23-2005 8:46 PM


Re: Not stopping, but slowing.
Errors are tools ?

Of course you are not using "tool" to mean its understood definition.

No, you are right. Tool is a bad term. What I usually use is substrate, as in 'Mutation introduces variation which acts as a substrate for natural selection'.

Isn't the age of the Earth really based upon the time needed for all the "errors" to produce what is seen today ?

Um, no. I would say almost certainly not, but feel free to provide some evidence if you feel that is the case.

Of course you have no evidence of RM outside of logic asserting it must of happened or how else did everything get here.

You mean apart from the many millions of instances of mutation as random as we are able to determine? There are hundreds of studies of point mutations and larger scale changes in bacterial clonal cultures, there are many studies of genetic mutations in children with spontaneous genetic defects.

It is arguable that these are not truly random, in that not every mutation is equally likely to happen, but they are random in as much as there are many effectively random variables feeding into the processes of mutation.

How does NS know to improve if it is not intelligent ?

Because, as Mangy Tiger pointed out to you, the only thing it improves is replication frequency, which is what natural selection does naturally. It is simply a mathematical phenomenon. All else being equal something with a faster reproductive rate will come to predominate in a population.

Isn't NS simply the naturalist god ?

No.

Isn't NS simply a euphemism for God ?

No, although many theistic evolutionists may choose to see RM/NS as a mechanism by which god can direct evolution. There is no reason why an omnipotent being couldn't cause a point mutation at just the right spot in the germ line of one organisms in order to establish a variant which will have an advantage in a different environment, something we would never be able to identify amongst the natural background noise of random mutations. That is the thing about being omnipotent you can do anything. That isn't a scenario one could ever disprove, which is why people who study evolution don't take it into consideration in the science they do, even if they happen to believe that is what is really happening.

TTFN,

WK


This message is a reply to:
 Message 25 by Cold Foreign Object, posted 05-23-2005 8:46 PM Cold Foreign Object has not yet responded

  
Wounded King
Member (Idle past 2515 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 30 of 35 (210790)
05-24-2005 4:58 AM
Reply to: Message 28 by Limbo
05-24-2005 1:12 AM


As we know evolution is a 'blind' process. Could the discovery of “preprogrammed” mechanisms of variation be interpreted as evidence for ID?

Yes. I think this could be very suggestive evidence for ID. The problem is one of defining 'pre-programmed'. Are we looking for something like a zipped file in the DNA? A short piece of sequence which some process will allow to be decompressed into a novel gene? Would you argue that the mechanism we see which act to direct hypermutation to some extent in response to environmental stress are 'pre-programmed'?

I think that the first of these would clearly be suggestive, although not neccessarily conclusive, evidence for ID. The second I would argue could easily be brought about by natural selection.

What is the relationship between the estimated length of time required for the evolutionary process and the estimated age of the earth?

I can't think of any, but Ray seems to think there is a connection. It is true that there were some arguments when scientific estimates were first being proposed that some figures, in the hundreds of millions, were too short to allow for evolution to have occurred. However the current techniques for dating have absoloutely nothing to do with evolution and the assumptions behind those early estimates have been shown to be mistaken.

Would “preprogrammed” mechanisms force us to re-evalute the age of the earth?

No.

TTFN,

WK


This message is a reply to:
 Message 28 by Limbo, posted 05-24-2005 1:12 AM Limbo has not yet responded

Replies to this message:
 Message 31 by Wounded King, posted 05-26-2005 5:33 AM Wounded King has not yet responded

  
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