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Author Topic:   the phylogeographic challenge to creationism
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 57 of 298 (263612)
11-27-2005 8:35 PM
Reply to: Message 47 by halucigenia
11-27-2005 6:33 PM


Re: A harder easy question
cute, but you didn't set the bar high enough.

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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 60 of 298 (263616)
11-27-2005 8:38 PM
Reply to: Message 56 by DrJones*
11-27-2005 8:34 PM


Re: A harder easy question
42

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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 166 of 298 (265567)
12-04-2005 9:36 PM
Reply to: Message 165 by mick
12-04-2005 6:34 PM


post extinction species explosions ...
There is another mechanism that may be in play with introduced species which doesn't necessarily apply to normal evolutionary processes.
In the study of foraminifera by Arnold and Parker
Geology Dept article 3
They had the opportunity to observe speciation explosions after the KT extinction event, and saw a proliferation of species diverging to fill the different foraminifera niches:
One of the last great extinctions occurred roughly 66 million years ago, and according to one popular theory it resulted from Earth's receiving a direct hit from a large asteroid. Whatever the cause, the event proved to be the dinosaurs' coup de grace, and also wiped out a good portion of Earth's marine life -- including almost all species of planktonic forams.
Like ecologists who study how wildlife recovers from a forest fire, evolutionists are drawn to such incidences of "biological vacuum" in search of clues as to how the earliest forms of life started evolving, when competition wasn't the controlling factor in the process.
s revealed by the ancient record left by the foram family, the story of recovery after extinction is every bit as busy and colorful as some scientists have long suspected.
"What we've found suggests that the rate of speciation increases dramatically in a biological vacuum," Parker said. "After the Cretaceous extinction, the few surviving foram species began rapidly propagating into new species, and for the first time we're able to see just how this happens, and how fast."
As foram survivors rush to occupy their new habitats, they seem to start experimenting will all sorts of body shapes, trying to find something stable, something that will work, Arnold said. Once a population in a given habitat develops a shape or other characteristic that stands up to the environment, suddenly the organisms begin to coalesce around what becomes a standardized form, the signature of a new species.
As the available niches begin to fill up with these new creatures, the speciation rate begins to slow down, and pressure from competition between species appears to bear down in earnest. The extinction rate then rises accordingly.
It seems to me that some (by no means all) introduced species are different enough from the native {flora\fauna} that they are in a "partial vacuum" situation and thus can diversify in a similar manner.

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.

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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 173 of 298 (265668)
12-05-2005 7:16 AM
Reply to: Message 167 by Faith
12-05-2005 2:12 AM


Re: post extinction species explosions ...
this is a non-sequitur to my post faith.
denial is not evidence either.

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Replies to this message:
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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 179 of 298 (265820)
12-05-2005 4:49 PM
Reply to: Message 176 by Faith
12-05-2005 1:30 PM


Re: post extinction species explosions ...
My post was about the explosion of species when there is a vacuum to fill, the fossils are irrelevant to the argument really, but substantiation for those of us who like it.
The topic involved was the observed increase in diversity in introduced species (to areas outside their natural occured area)
They too could experience a similar {vacuum\fill} response if they are different enough from the native {flora\fauna} of the area introduced into, such that they could 'explode' into the introduced area. examples: rabbits in australia, starlings in america.
(Both of these species (and others) btw demonstrate the mechanims of punk eek whereby a new species can suddenly appear in a short time, where the founding population is small and where the formation of the new species has not been recorded.)
If they are not confined to as small a niche as they were previously then they can respond with greater diversity before natural selection pulls in the reins.

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 176 by Faith, posted 12-05-2005 1:30 PM Faith has replied

Replies to this message:
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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 188 of 298 (266013)
12-06-2005 7:43 AM
Reply to: Message 184 by Faith
12-06-2005 2:54 AM


Re: post extinction species explosions ...
I was responding to micks post on increased diversity with introduced species compared to species in their native habitat.
his post
EvC Forum: the phylogeographic challenge to creationism
my post
EvC Forum: the phylogeographic challenge to creationism
The foraminifer were an example of species surviving an extinction event differentiating with less barriers to diversity because there was a vacuum to fill.
My point was that in some cases an introduced species would be in a similar situation if there were a partial vacuum -- no natural predators for instance, as occurred with the rabbits in australia and the starlings in the US.
The point is not so much about phenotype\genotype\alleles but about the smaller pressure from natural selection allowing more diversity to occur.

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.

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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 206 of 298 (266238)
12-06-2005 10:33 PM
Reply to: Message 189 by Modulous
12-06-2005 10:43 AM


Re: Evolution=Random Mutation + Selection (E=1+x-y)
I would say evolution = species + changes - selection, and write the equation as
E2 = E1 + C - S
This allows you to include genetic drift and environmental effect on the expression of genes during development, especially if they result in copy errors for their descendents, and any other sources of change with mutations.
A mother passes resistance to diseases to her child in the milk, not the genes, and there are other factors (like diet) that affect fitness survival rather than just the number of available allele modules.
In each generation C and S are independent, sometimes one bigger than the other other times not.
I also think that if you remove selection from the equation that you end up with just as much problems as removing mutation.
Are copy errors being considered mutations here? I don't think they can be so considered, as only the offspring with the errors can "inherit" them, while other offspring would have their own errors.
just some thoughts.

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.

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Replies to this message:
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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 207 of 298 (266241)
12-06-2005 10:43 PM
Reply to: Message 205 by TimChase
12-06-2005 2:16 PM


Re: Ring Species
The two populations will diverge, then tend to adapt to different environments and different pressures. At some point, even if the two species come into contact with one-another, they will no longer be able to produce fertile offspring -
Or recognise the others as potential mates even if they were able to produce fertile offspring. This is in essence what has happened with the asian greeshish warblers where the two ends overlap. The change in song and coloring is enough that they do not see the others as {our-type}
Once inter-breeding fails - for whatever reason - divergence continues.

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.

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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 232 of 298 (266541)
12-07-2005 6:45 PM
Reply to: Message 208 by Cal
12-07-2005 12:25 AM


Re: copy errors = mutations or random mistakes.
Are copy errors being considered mutations here?
Why wouldn't they be?
Because they aren't changes in the parent that are passed on after survival to reproduction status, and they are mistakes in the making of a single organism, but not in the rest of the sibling offspring.
The flip side is that you can call all changes mutations, and this makes it simple for those who don't want to take too much trouble to understand the different mechanisms available, but it also makes it more difficult to then distinguish the effects of the different kinds of changes when some do and some don't.
To me it's a matter of communication and definition. The better you define a problem the better you will be at finding a solution.
It seems to me that changes to the proportions of alleles available in populations is due to:
  • mutations in the genes of the parent stock
  • copy errors in the transmission of genes to the offspring stock
  • genetic drift due to the random 50-50 choice of which parent gene of each parent is passed to the offspring stock
It seems to me that copy error is between mutation and genetic drift and has some elements of each, thus this distinction may be critical in understanding some disease aspects (especially if there are {chemical\environmental} factors that can cause copy errors). Of course you could have a mutation that causes copy errors ...
Are there other mechanisms for change?

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.

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Replies to this message:
 Message 233 by mick, posted 12-07-2005 6:57 PM RAZD has replied
 Message 234 by Wounded King, posted 12-07-2005 7:06 PM RAZD has replied

  
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 236 of 298 (266554)
12-07-2005 8:13 PM
Reply to: Message 234 by Wounded King
12-07-2005 7:06 PM


Re: copy errors = mutations or random mistakes.
I'm assuming that by 'mutation' you mean a change in the primary sequence of DNA
That's my take on it, yes. The other difference I see is that mutation affects single sites with {plus\minus\delta} possibilities (where delta is a substitution), while copy errors are ones that can reproduce whole segments of DNA, copies of necessary areas now able to become new features.
such as DNA methylation
Interesting. Works as a means to preserve genetic function?

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:
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Replies to this message:
 Message 237 by pink sasquatch, posted 12-07-2005 11:53 PM RAZD has replied
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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 261 of 298 (267305)
12-09-2005 6:41 PM
Reply to: Message 238 by Wounded King
12-08-2005 4:31 AM


Re: copy errors =
Are you defining 'copy' errors as ...
For the record, I use copy errors to mean error in the reproduction of the DNA during the reproduction process, whether it adds or deletes segments or places then in the wrong order or direction.

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Replies to this message:
 Message 263 by Wounded King, posted 12-09-2005 6:54 PM RAZD has replied

  
RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 262 of 298 (267306)
12-09-2005 6:44 PM
Reply to: Message 237 by pink sasquatch
12-07-2005 11:53 PM


Re: copy errors = mutations or random mistakes.
Strictly speaking, a "mutation" is any genetic sequence (or lack thereof) in an offspring that does not match the portion of genome inherited from its parent(s).
Pehaps a little overstated: this is only copy errors by my definitions, and does not include changes that have occurred in the parent DNA since it's inception ...

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 237 by pink sasquatch, posted 12-07-2005 11:53 PM pink sasquatch has replied

Replies to this message:
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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 264 of 298 (267313)
12-09-2005 6:59 PM
Reply to: Message 233 by mick
12-07-2005 6:57 PM


Re: copy errors = mutations or random mistakes.
The third sentence isn't right at all; genetic drift is not due to random segregation of chromosomes, it's due to stochastic factors like a tree falling on some animal's head when that animal lives in a small population.
from wikipedia:
Genetic drift is a contributing factor in biological evolution, in which traits which do not affect reproductive fitness change in a population over time. Whereas natural selection causes traits to becomemore prevalent when they contribute to fitness, or eliminates those which harm it, genetic drift is a somewhat random process which affects traits that are more neutral.
Genetic drift is a statistically stochastic process that arises from the role of random sampling in the production of offspring. The genes of each new generation are not a simple copy of the genes of the successful members of the previous one, but rather a sampling, which includes some statistical error. Drift is the cumulative effect over time of this sampling error on the allele frequencies in the population.
This random sampling error would include both your tree falling by a totally random process on an unfortunate victim and the random ommission of one parents genes in the reproduction process, more likely the fewer offspring the parent has.
ie -- not all the genes that are lost from one generation to the next are due to selection factors, and those that are due to random factors are lumped together into genetic drift.

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:
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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 266 of 298 (267339)
12-09-2005 8:35 PM
Reply to: Message 265 by pink sasquatch
12-09-2005 8:10 PM


Re: clarifying mutation terms
It does include most somatic mutations when you consider a daughter cell to be "offspring" of a parent cell (within the same organism); but to be clear I was specifically referring to mutation in the sense of heredity.
Which should include all the changes in the DNA accumulated by the parent up to the moment of reproduction - the mutations in it's DNA that have occurred over time since it's {birth\inception}. You seemed to have only included changes during reproduction, hence the comment about overstatement.
I chose to distinguish between source changes (reflected in all offspring that get the gene (allowing for sex randomness)) and copy changes (reflected in single offspring). Calling it all mutation to me muddies the waters and is an unnecessary if not counterproductive oversimplification.
You seemed to originally be using "copy errors" ...
For any error in making a copy of the DNA during the process of reproduction. Whether duplication, deletion, inversion or whatever.
Duplication of course gives the possibility of future change to one copy while leaving the other for its original purpose.

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 265 by pink sasquatch, posted 12-09-2005 8:10 PM pink sasquatch has replied

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RAZD
Member (Idle past 1434 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 267 of 298 (267343)
12-09-2005 8:40 PM
Reply to: Message 263 by Wounded King
12-09-2005 6:54 PM


Re: copy errors =
You seem to be making a fairly arbitrary distinction here.
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?

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 263 by Wounded King, posted 12-09-2005 6:54 PM Wounded King has replied

Replies to this message:
 Message 269 by pink sasquatch, posted 12-09-2005 9:29 PM RAZD has replied
 Message 270 by TimChase, posted 12-09-2005 10:06 PM RAZD has replied
 Message 271 by Wounded King, posted 12-10-2005 3:08 AM RAZD has replied

  
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