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Author Topic:   the phylogeographic challenge to creationism
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 271 of 298 (267430)
12-10-2005 3:08 AM
Reply to: Message 267 by RAZD
12-09-2005 8:40 PM


Re: copy errors =
In one case you have mutations - changes - happening to DNA in a random process independent of reproduction. Radiation whatever.
In the other case you have mistakes made in the replication of the DNA.
How is this difference arbitrary?
Because these aren't 2 different cases. Virtually every single instance of a mutation of any kind, point, inversion, duplication, deletion is the result of the process of DNA replication. When mutagenic factors alter DNA they frequently only affect 1 strand and the alteration they produce is frequently not a chemical conversion of a nucleotide to a totally different valid nucleotide but to a particularly chemically altered form of the original nucleotide or an aberant form of a different nucleotide (Alberts, et al, 2002).It is only when the DNA is copied and a new strand syntesised using the altered nucleotide as a template that a proper complementary nucleotide is introduced into the base pair, and only after a subsequent round of reproduction that a double strand will be produced with 2 properly complementary normal nucleotides.
Arguably retroviral insertions don't require DNA synthesis, at least on the part of the host cell, but in the almost all classes of mutation rely on DNA synthesis, or replication, to effect a valid change in the coding sequence.
That is why your distinction is arbitrary, because the processes you categorise in 1, 'radiation whatever', are also the result of your category 2 'mistakes made in the replication of DNA'.
TTFN,
WK

This message is a reply to:
 Message 267 by RAZD, posted 12-09-2005 8:40 PM RAZD has replied

Replies to this message:
 Message 272 by RAZD, posted 12-10-2005 8:58 AM Wounded King has not replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 272 of 298 (267477)
12-10-2005 8:58 AM
Reply to: Message 271 by Wounded King
12-10-2005 3:08 AM


Re: copy errors = off topic
this should be another topic.
{abe} I have added a new topic at
EvC Forum: changes vs mutations ... perhaps clarifying the terms in the process.
to discuss this issue {/abe}
{dbe}(moved to above thread){dbe}
This message has been edited by RAZD, 12*10*2005 10:41 AM

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

This message is a reply to:
 Message 271 by Wounded King, posted 12-10-2005 3:08 AM Wounded King has not replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 273 of 298 (267485)
12-10-2005 9:37 AM
Reply to: Message 259 by Faith
12-09-2005 12:02 PM


More off topic posts
Guilty.
It is just too easy to respond to a post and forget about the topic above the post.
Sorry Mick.

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

This message is a reply to:
 Message 259 by Faith, posted 12-09-2005 12:02 PM Faith has not replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 274 of 298 (267505)
12-10-2005 10:51 AM
Reply to: Message 270 by TimChase
12-09-2005 10:06 PM


Re: copy errors = new topic
thanks for the open approach at least
I have started a new thread on this topic at
http://EvC Forum: changes or mutations ... perhaps clarifying the terms in the process.
perhaps you would care to adjust and reply there? then we can leave this to Micks excellent topic.

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

This message is a reply to:
 Message 270 by TimChase, posted 12-09-2005 10:06 PM TimChase has not replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 275 of 298 (267515)
12-10-2005 11:25 AM
Reply to: Message 269 by pink sasquatch
12-09-2005 9:29 PM


Re: copy errors =
see http://EvC Forum: changes or mutations ... perhaps clarifying the terms in the process. -->EvC Forum: changes or mutations ... perhaps clarifying the terms in the process.
for more discussion on this issue.
rather than get confused by the {mutation = all changes} issue this first is discussing what different mechanism exist for change to DNA.

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 Message 269 by pink sasquatch, posted 12-09-2005 9:29 PM pink sasquatch has not replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 276 of 298 (268109)
12-12-2005 10:14 AM
Reply to: Message 172 by Mammuthus
12-05-2005 6:08 AM


back for a little while
bump

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 277 of 298 (270481)
12-18-2005 11:01 AM
Reply to: Message 240 by TimChase
12-08-2005 9:50 AM


Re: Ring Species
It's been hard to get back to this post because it's SO long and the thread went off topic and now SO much time has elapsed but maybe I'll try a short response.
TimChase writes:
Well, what is neat about [ring species] is the fact that it demonstrates speciation in action in a way that in a certain sense is frozen in time, so that any time one visits the place, one can see the living evidence.
Faith writes:
quote:
But evidence of what? Of that fact that species vary phenotypically, sometimes to extremes? This is commonplace. The process that brings it about is the subtractive process under discussion which gives the lie to the idea that the ordinary processes of variation and selection demonstrate evolution.
.. As for the "subtractive process under discussion which gives lie" to anything, this is simply your unsupported assertion.
It's a logical inference from the processes in question, nothing so grand as an unsupported assertion.
2. Mutations are quite common, even harmless ones.
The question that keeps being raised about mutations here at EvC is whether or not they are random events as opposed to law-abiding processes that are predictable. To the extent they are the latter they can't be said to be bringing anything new into the species picture, but merely contributing to the built-in variability that all living things exhibit through Mendelian processes, dominance-recession and so on.
In fact they are so common that we will be using them to trace the lineage of cells in embryonic and oncological development:
But this is off the topic of the OP so I won't be tracing it with you.
Wipe out that which connects the two extremes and they are no longer members of the same species -- but are they members of the same species while the bridge exists? Well, yes and no. Is cyan blue or is it green? At this point, we are asking the wrong question.
quote:
That's not a question I'm asking.
If you were concerned with how speciation takes place, it would be.
I believe speciation has a natural limit defined by the fact that most of the processes that lead to speciation, from genetic drift to natural selection to bottleneck, produce new phenotypes BY reducing genetic variability. Mutation keeps being added in without the slightest attempt to explain how it might overcome this effect, rather it appears to be assumed.
Additionally, oftentimes those who deny the reality of macroevolution will do so at the level of species, claiming that one species cannot evolve into two. Or maybe they pick a somewhat higher level, such as denying that an autocatalytic RNA strand (essentially, a viroid with the ability to reproduce) could ever evolve into a human being. But once one admits speciation, the rest is largely just a matter of degree.
That is merely the ToE faith. The processes I am discussing tend to limit speciation past a certain point call this faith into question.
So goes the theory, but if the processes that bring about speciation simultaneously reduce the genetic diversity that evolution requires (beyond the mere variation on given genetic allotments), and mutation turns out not to be a sufficiently effective counter to this subtraction process, then this theory of an open-ended evolution is falsified.
quote:
3. From the above paragraph, "if the processes that bring about speciation reduce the genetic diversity... and mutation turns out not to be a sufficiently effective counter to this subtraction process, ... then this theory ... of ... evolution is falsified." Yes. "If" such conditions were true, "then" this "open-ended" evolution would be falsified. That is science. In contrast to pseudo-science which typically fails to make any predictions, science makes predictions and is falsifiable. But being falsifiable is not the same thing as being falsified. Real empirical science is based upon the the evidence, and it stands or falls with the evidence.
My statement was logically correct and I suggest you review it.
I'll have to get back to this as it's taking too long and I have to go to church.

This message is a reply to:
 Message 240 by TimChase, posted 12-08-2005 9:50 AM TimChase has not replied

Replies to this message:
 Message 278 by crashfrog, posted 12-18-2005 3:52 PM Faith has replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 278 of 298 (270545)
12-18-2005 3:52 PM
Reply to: Message 277 by Faith
12-18-2005 11:01 AM


Re: Ring Species
The question that keeps being raised about mutations here at EvC is whether or not they are random events as opposed to law-abiding processes that are predictable. To the extent they are the latter they can't be said to be bringing anything new into the species picture, but merely contributing to the built-in variability that all living things exhibit through Mendelian processes, dominance-recession and so on.
It's not clear to me what additional evidence would be neccesary to prove to you that, in fact, it's been proven that mutations are fundamentally random and not the product of predictable law-abiding processes. But I should think the fact that we observe variation within species beyond, that cannot be explained by, the basic Mendelian mechanisms of dominance/recession (which largely don't apply to the majority of genes, anyway), would be sufficient to do so.
You might just as well assert that airplanes cannot possibly exist, because Bernoulli's principle doesn't provide enough lift. And yet, the airplanes fly. What you need to understand is, when your conception of things leads logically to conclusions that are demonstratably untrue, that's proof that you're wrong.
Mutation keeps being added in without the slightest attempt to explain how it might overcome this effect, rather it appears to be assumed.
We've already explained how mutations overcome this effect. But, to repeat: mutations overcome the contraction of genetic diversity via natural selection by increasing genetic diversity.
It's really very simple. What part of that are you having trouble with? You don't understand how a mutation increases genetic diversity?
My statement was logically correct and I suggest you review it.
It's logically correct, but it's been proven that mutation overcomes the contraction of diversity in gene pools that result from selective processes. Proven about 200 posts ago, as I seem to recall, and as yet, unchalleneged by you or any of your peers.
Can we dismiss the fiction that mutation doesn't provide enough diversity to overcome selection, now?

This message is a reply to:
 Message 277 by Faith, posted 12-18-2005 11:01 AM Faith has replied

Replies to this message:
 Message 279 by Faith, posted 12-18-2005 5:01 PM crashfrog has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 279 of 298 (270562)
12-18-2005 5:01 PM
Reply to: Message 278 by crashfrog
12-18-2005 3:52 PM


Re: Ring Species
It has not been proven. Many speculations, no proof. Others, not just creos, have said things that disagree with you.
We've already explained how mutations overcome this effect. But, to repeat: mutations overcome the contraction of genetic diversity via natural selection by increasing genetic diversity.
In a complex system with one factor increasing diversity and half a dozen decreasing it so much is possible that you need to say more than this. And that one factor that increases it does so sometimes in a random way, often in a lethal way, sometimes in a neutral way, rarely in a positive way, and a lot of it doesn't look random at all but predictable.
This message has been edited by Faith, 12-18-2005 05:23 PM
This message has been edited by Faith, 12-18-2005 06:01 PM

This message is a reply to:
 Message 278 by crashfrog, posted 12-18-2005 3:52 PM crashfrog has replied

Replies to this message:
 Message 280 by crashfrog, posted 12-20-2005 12:22 AM Faith has replied
 Message 282 by nwr, posted 12-20-2005 12:45 AM Faith has replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 280 of 298 (270975)
12-20-2005 12:22 AM
Reply to: Message 279 by Faith
12-18-2005 5:01 PM


Re: Ring Species
It has not been proven. Many speculations, no proof.
The proof, as I said, has been presented. Mutations are random; we know this because random mutations, with random fuctions, occur whether or not they represent a survival advantage to the organism. And we know that they're not the result of some pre-programmed cellular mechanism because if they were, the clonal decendants of a single organism would never develop diversity, because they'd all develop the same mutations at the same time (because, being clonal, they have the same cellular mechanism.)
It's proven that mutations are random, and not the result of the processes you describe. If you wish to challenge this point, by all means do so with evidence. But simple protestations of "nu-uh!" and "I heard you're wrong!" don't constitute anything but fallacious appeals to ignorance and anonymous "authorities."
Others, not just creos, have said things that disagree with you.
Not really. If you read it that way it's because you're not educated enough to understand what people are telling you. That you lack any basis of knowledge in regard to physical chemistry and genetics was made abundantly clear, as you'll recall, when you misinterpreted the abbreviations for nucleotides in a codon as the abbreviations for elements in a molecule.
In a complex system with one factor increasing diversity and half a dozen decreasing it so much is possible that you need to say more than this.
No, you don't. Mutation provides enough diversity to counteract your "half a dozen" diversity-contracting mechanisms - a fact that has been abundantly proven to you.
And that one factor that increases it does so sometimes in a random way, often in a lethal way, sometimes in a neutral way, rarely in a positive way, and a lot of it doesn't look random at all but predictable.
It's predictably random, which proves my point. Moreover the fact that some mutations are lethal is irrelevant. We're talking about diversity, not fitness.

This message is a reply to:
 Message 279 by Faith, posted 12-18-2005 5:01 PM Faith has replied

Replies to this message:
 Message 281 by Faith, posted 12-20-2005 12:41 AM crashfrog has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 281 of 298 (270978)
12-20-2005 12:41 AM
Reply to: Message 280 by crashfrog
12-20-2005 12:22 AM


Re: Ring Species
Come on, crashie, you simply need to REALLY prove it SO carefully to li'l 'ol ignorant me. Surely you know that it takes much repetition and careful explanation and many different approaches to educate a person in the complexities of genetics. Patience.
This message has been edited by Faith, 12-20-2005 12:45 AM

This message is a reply to:
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Replies to this message:
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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 282 of 298 (270981)
12-20-2005 12:45 AM
Reply to: Message 279 by Faith
12-18-2005 5:01 PM


Re: Ring Species
Faith writes:
In a complex system with one factor increasing diversity and half a dozen decreasing it so much is possible that you need to say more than this.
If you have some factors increasing diversity, and others decreasing diversity, you would expect some sort of equilibrium.
When there is very little diversity present, the factors that decrease diversity won't have much effect, since there isn't much to decrease. Thus the factors that increase diversity will tend to dominate. Conversely, if there is a lot of diversity, then the factors that decrease will tend to dominate. It should settle down at a somewhat stable level of diversity.
And that one factor that increases it does so sometimes in a random way, often in a lethal way, sometimes in a neutral way, rarely in a positive way, and a lot of it doesn't look random at all but predictable.
If a species is already well adapted to its environment, then it is to be expected that most mutations will be negative or neutral. This is a bit like the saying "if it ain't broke, don't fix it." If things are working reasonably well, and something changes, the change is more likely to be for the worse.
If the species is less well adapted, then there is room for improvement so it is statistically more probable that some of the mutations will be beneficial.
If the environment changes in such a way that the species is less well adapted to the changed environment then, as the paragraph above indicates, there will be more room for improvement so more of the random mutations will be beneficial. This helps the species adapt to the changed environment.

Impeach Bush.

This message is a reply to:
 Message 279 by Faith, posted 12-18-2005 5:01 PM Faith has replied

Replies to this message:
 Message 283 by pink sasquatch, posted 12-20-2005 1:15 AM nwr has replied
 Message 284 by Faith, posted 12-20-2005 1:19 AM nwr has replied

  
pink sasquatch
Member (Idle past 6022 days)
Posts: 1567
Joined: 06-10-2004


Message 283 of 298 (270989)
12-20-2005 1:15 AM
Reply to: Message 282 by nwr
12-20-2005 12:45 AM


equilibrium
An excellent post, nwr, covering many important ideas concisely and understandably. I'll try to add some detail that hopefully you'll find interesting:
When there is very little diversity present, the factors that decrease diversity won't have much effect, since there isn't much to decrease. Thus the factors that increase diversity will tend to dominate. Conversely, if there is a lot of diversity, then the factors that decrease will tend to dominate.
Dobzhansky demonstrated this in the 1950's with fruit fly experiments. He took several pairs of fruit flies from a large colony and used them to seed new colonies - creating a series of severe bottlenecked populations. These bottlenecked populations consistently and rapidly became more phenotypically variable than the founder population, which stayed relatively stable. (This is one of those classic papers I wish I could find on-line...)
If a species is already well adapted to its environment, then it is to be expected that most mutations will be negative or neutral. This is a bit like the saying "if it ain't broke, don't fix it." If things are working reasonably well, and something changes, the change is more likely to be for the worse.
Yes - this is called "normalizing" or "neutralizing" selection; that is, selection that maintains the status quo. Most species can be thought of as "optimized" given their long evolutionary histories - which is why we rarely directly observe beneficial mutations.
If the environment changes in such a way that the species is less well adapted to the changed environment then, as the paragraph above indicates, there will be more room for improvement so more of the random mutations will be beneficial.
That's when normalizing selection ceases - with a change to the environment. This is why our examples of recent beneficial mutations often are the result of new environments being created by man - mutations to resist pesticides or antibiotics, or to use a synthetic like nylon as a food source.

This message is a reply to:
 Message 282 by nwr, posted 12-20-2005 12:45 AM nwr has replied

Replies to this message:
 Message 285 by nwr, posted 12-20-2005 1:44 AM pink sasquatch has not replied
 Message 289 by Faith, posted 12-20-2005 3:00 AM pink sasquatch has not replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 284 of 298 (270990)
12-20-2005 1:19 AM
Reply to: Message 282 by nwr
12-20-2005 12:45 AM


Re: Ring Species
In a complex system with one factor increasing diversity and half a dozen decreasing it so much is possible that you need to say more than this.
quote:
If you have some factors increasing diversity, and others decreasing diversity, you would expect some sort of equilibrium.
This remains to be proved.
When there is very little diversity present, the factors that decrease diversity won't have much effect, since there isn't much to decrease.
It's when there is very little diversity left that the phenomenon I'm talking about is on display as it were. At this point we have speciation to the max. There is no further variation possible, unless mutation can increase the diversity to the point that further speciation is again possible. Otherwise it is at this point that extinction becomes a real possibility if the environment requires a change that can't occur. The opposite of what evolution would predict.
Thus the factors that increase diversity will tend to dominate.
If extinction doesn't occur. If extreme bottleneck doesn't occur. What is needed is some real conjuring with actual facts and possibilities.
Conversely, if there is a lot of diversity, then the factors that decrease will tend to dominate. It should settle down at a somewhat stable level of diversity.
But doesn't death itself reduce diversity over time? Every individual that dies without reproducing would either make no difference or makes a small difference -- in the direction of reducing genetic potentials. It represents some genetic potential that is no longer available in the gene pool, to however small a degree. At least even a single death changes frequencies in the population as all these factors I've been talking about do.
And that one factor that increases it does so sometimes in a random way, often in a lethal way, sometimes in a neutral way, rarely in a positive way, and a lot of it doesn't look random at all but predictable.
quote:
If a species is already well adapted to its environment, then it is to be expected that most mutations will be negative or neutral. This is a bit like the saying "if it ain't broke, don't fix it." If things are working reasonably well, and something changes, the change is more likely to be for the worse.
Interesting point. This of course means that mutation in this situation becomes a factor not of increased diversity but of decreased viability and therefore eventually decreased diversity, if it is true that any death before reproduction, if it has any effect at all, will have an effect in that direction. It is even possible at an extreme for a death to remove from a very small population the last remaining alternate allele for a particular trait, leaving that population totally homozygous for that trait and incapable of variation unless a truly useful mutation can be counted on. Some have said that this kind of mutation is actually rather common. In which case I don't think we're talking about mutation but some kind of built-in mechanism that contributes to variation in a nonrandom way.
There's a lot I need to learn I know, but everything in its time. If these processes aren't acknowledged I'm not going to be able to learn the processes that supposedly oppose them as it's like denying that this is going on at all, and I simply have to repeat it.
If the species is less well adapted, then there is room for improvement so it is statistically more probable that some of the mutations will be beneficial.
If the environment changes in such a way that the species is less well adapted to the changed environment then, as the paragraph above indicates, there will be more room for improvement so more of the random mutations will be beneficial. This helps the species adapt to the changed environment.
What you mean by "beneficial" seems to be merely that they will more likely produce a change that will be expressed phenotypically, but what's to guarantee that the new trait will be useful in some adaptive way?
And what in reality is actually seen? This is pretty speculative.

This message is a reply to:
 Message 282 by nwr, posted 12-20-2005 12:45 AM nwr has replied

Replies to this message:
 Message 287 by crashfrog, posted 12-20-2005 1:57 AM Faith has replied
 Message 292 by nwr, posted 12-20-2005 10:58 AM Faith has replied

  
nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 285 of 298 (270995)
12-20-2005 1:44 AM
Reply to: Message 283 by pink sasquatch
12-20-2005 1:15 AM


Re: equilibrium
Thanks for your comments. It is always interesting to see data that fits one's pet theories.
As you recognized, I was trying to make things a little clearer for Faith. Since she has replied, I hope that indicates my post helped.
Note to Faith: I will respond in some detail to your recent reply, but it won't be till tomorrow. It's getting a tad late here.

This message is a reply to:
 Message 283 by pink sasquatch, posted 12-20-2005 1:15 AM pink sasquatch has not replied

  
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