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Author Topic:   Introduction to Genetics
RAZD
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(1)
Message 95 of 236 (719499)
02-14-2014 2:49 PM
Reply to: Message 90 by Faith
02-14-2014 1:09 PM


Re: Speciation = scientific macroevolution
No, I guess I need to say it every time it comes up, I do not regard speciation as macroevolution, it is an event that does occur though so I keep the name for it, but it is merely a population, a race, of a particular species that has lost its ability to interbreed with others of that species, probably most often due to changes in the genome. And the kicker is that it should have less, little or no ability to vary further, making it an odd misnomer within the ToE anyway.

And once again, the only one you deceive is yourself: scientists and scientifically literate know that this is the scientific definition for macroevolution.

If you want to invent a new word, you can make up something for your fantasy version that you keep denying occurs.

Curiously I find it amusing that the longer these debates go, the more creationists accept basic evolutionary processes, especially if they can call them something else ...

It's like it's not evolution per se that is denied, just the words used by evolutionary scientists ...


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This message is a reply to:
 Message 90 by Faith, posted 02-14-2014 1:09 PM Faith has responded

Replies to this message:
 Message 96 by Faith, posted 02-14-2014 3:28 PM RAZD has responded

  
RAZD
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Posts: 20110
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.9


Message 99 of 236 (719509)
02-14-2014 3:59 PM
Reply to: Message 96 by Faith
02-14-2014 3:28 PM


Re: This thread should be about facts not interpretaions
Insisting on definitions does not belong on this thread. I'm a creationist and I have a different way of understanding the data than you do and your attempt to force it down my throat is unwelcome, especially on this thread. Get off this thread.

Curiously I am not insisting on definitions, just pointing out that when you use a word that is commonly understood to mean something else then you are not communicating clearly, and then you end up complaining later about how people don't understand your points.

So you now concede that both microevolution and speciation occur as part of the natural world post flood ... wonderful.

The theory of evolution can be stated as the theory that microevolution and speciation are sufficient to explain the diversity of life as we know it.

You are well on your way -- here and on some of the other threads -- to demonstrating that you believe this is sufficient to explain the diversity of life since the flood.

As I said, you are being forced by reality to either acknowledge basic evolution or deny reality.

Get off this thread.

Funny.

Message 94: ... Not mutations yet, let's just stick to what had already been brought up. ...

ANY change to DNA is a mutation, so you are well into mutations already. Baulking at words that describe what you have been describing is not argument but denial.

Just look at your aversion to the word "divergence" in [msg=719395] ... most amusing the length you went to.

But if you want to discuss Message 116 I'll be glad to leave you along here.


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This message is a reply to:
 Message 96 by Faith, posted 02-14-2014 3:28 PM Faith has responded

Replies to this message:
 Message 101 by herebedragons, posted 02-14-2014 4:23 PM RAZD has responded
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RAZD
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Joined: 03-14-2004
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(2)
Message 102 of 236 (719516)
02-14-2014 4:29 PM
Reply to: Message 101 by herebedragons
02-14-2014 4:23 PM


Re: This thread should be about facts not interpretaions
I know. Let's talk about human / chimp relatedness but don't bring up mutations and don't use evolutionary language. Talk about stacking the deck.

Well of course, and she'll be happy to talk about change but not mutation ... or speciation but not macroevolution ...


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RAZD
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Posts: 20110
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Joined: 03-14-2004
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(1)
Message 129 of 236 (719581)
02-15-2014 11:04 AM
Reply to: Message 104 by Faith
02-14-2014 4:47 PM


speciation, macroevolution and genetics
Speciation is not macroevolution and it isn't necessary to use that term. It's also not speciation either but I can't see a way to change that term, so I'll just have to keep writing out my view of it.

To be honest Faith, speciation isn't macroevolution so much as the beginning of it, so it is the dividing line as it were, between micro and macro.

So I would also be happy to avoid use of the term "macroevolution" until we can agree on what the term means (and that would likely take a new thread to figure out.

There is no concession involved; I've viewed it this way for years and I'm sure I must have said so years ago already even here.

So to summarize then, we are in agreement that -- to use a genetic definition for this thread:

(1) The process of (micro)evolution involves changes in the composition and the frequency of the distribution of alleles within breeding populations from generation to generation.

ie -- variation and adaptation, and this would include loss of alleles as well as redistributions.

And:

(2) The process of speciation involves the division of a parent population into two or more reproductively isolated daughter populations, which then are free to (micro) evolve independently of each other.

ie -- separation of breeding subpopulations by reproductive isolation.

In addition there would be variations within breeding populations that show diversity without being reproductively isolated subpopulations.

And where breeding populations means organisms reproducing after their kind\clade.

Except that there is nothing new about my view of these things, and speciation is not speciation, and there are many subspecies that belong to that diversity that aren't the product of speciation.

Subpopulations that are not reproductively isolated would be variations\varieties within reproductively isolated populations, but not able to interbreed with other reproductively isolated subpopulations, yes?

You would have:

  1. Kind/Clade -- a parent breeding population
    1. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation

Would you agree that isolation could be geographic (physical barriers to interbreeding) as well as genetic (loss of ability to interbreed)?

Would you agree that there could still be gene flow between varieties within a breeding subpopulation (ie hypbrids and new varieties)?

It is important that I use words that say what I mean and avoid sounding like I agree with evolutionist concepts I don't agree with. It is not an easy task to negotiate these differences between the models, ABE: especially in the teeth of the militant insistence on evolutionist terms as factual, which they are not /ABE. In the case of mutations, I do NOT agree that alleles are the product of mutations, they are built in variants of genes, built in from the Creation. Mutations hardly ever, and probably in actuality never, create viable alleles that perform the functions of normal alleles. Mutations may manage not to destroy their function, that is, they may be "neutral," or they may be many degrees of deleterious to the gene, or they might even bring about the death of a gene, which I think is how some of the junk DNA was formed (though I think most of it reflects the mass death of the Flood bottleneck), and the mere assumption that any allele was the product of mutation should be avoided on this thread. If there is some reason to assert it then it should be asserted and not assumed. But most of the time I don't see that there would be any reason to assert it at all. The idea that there is EVIDENCE that alleles are the product of mutation is false, but if someone wants to defend that then it should come up when we finally get to mutations.

What I have understood from past conversations is that you basically believe that all change within a kind/clade is through loss of alleles from some parent population as populations spread out and become isolated.

We will just have to disagree on whether mutations can add new alleles, because as far as I am concerned the evidence is compelling.

I'm not amused. "Divergence" is an evolution-specific word. Simple factual comparisons of differences between the genomes of different species are all that's needed on this thread.

Yet two subpopulations that have become reproductively isolated have -- by definition -- diverged from one another.

Would you be happier to use "separation\separated" or "deviation"?


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RAZD
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Joined: 03-14-2004
Member Rating: 3.9


Message 133 of 236 (719590)
02-15-2014 5:20 PM
Reply to: Message 130 by Faith
02-15-2014 4:35 PM


One issue I have with the concept is that I would expect it to show the trend to decreased genetic variability because it's a product of a population split or even a series of population splits, so that to call it a new "species" which implies it's a step in the process of evolution on to further species, is a tad overly optimistic.

Yes, this is a prediction of your hypothesis that all variation in a kind is pre-built into the ark-kind pair and that all subsequent speciation is due solely to loss of alleles as the offspring spread out. That we don't see a decrease in genetic variability would mean your hypothesis is falsified or at the least severely challenged.

"Speciation" implies something other than the usual development of a subspecies, ...

Nope.

... it implies something outside the Kind or Species itself, ...

Never.

Evolution is always within clades\kinds, and it is always surprising that creationists don't know this.

... (and having skimmed ahead a bit I see that RAZD is going to claim just that), ...

Perhaps you better re-read it then.

Subpopulations that are not reproductively isolated would be variations\varieties within reproductively isolated populations, but not able to interbreed with other reproductively isolated subpopulations, yes?

You would have:

  1. Kind/Clade -- a parent breeding population
    1. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation

Perhaps I should expand it ...

Subpopulations that are not reproductively isolated would be variations\varieties within reproductively isolated populations, but not able to interbreed with other reproductively isolated subpopulations, yes?

You would have:

  1. Kind/Clade -- a parent breeding population
    1. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation
      2. Variation/variety -- non-reproductively variation within a subpopulation
      3. Variation/variety -- non-reproductively variation within a subpopulation

    2. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation
      2. Variation/variety -- non-reproductively variation within a subpopulation
      3. Variation/variety -- non-reproductively variation within a subpopulation

    3. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation
      2. Variation/variety -- non-reproductively variation within a subpopulation
      3. Variation/variety -- non-reproductively variation within a subpopulation

  2. Kind/Clade -- a parent breeding population
    1. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation
      2. Variation/variety -- non-reproductively variation within a subpopulation
      3. Variation/variety -- non-reproductively variation within a subpopulation

    2. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation
      2. Variation/variety -- non-reproductively variation within a subpopulation
      3. Variation/variety -- non-reproductively variation within a subpopulation

    3. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation
      2. Variation/variety -- non-reproductively variation within a subpopulation
      3. Variation/variety -- non-reproductively variation within a subpopulation

  3. Kind/Clade -- a parent breeding population
    1. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation
      2. Variation/variety -- non-reproductively variation within a subpopulation
      3. Variation/variety -- non-reproductively variation within a subpopulation

    2. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation
      2. Variation/variety -- non-reproductively variation within a subpopulation
      3. Variation/variety -- non-reproductively variation within a subpopulation

    3. Speciation/subspecies -- a reproductively isolated subpopulation
      1. Variation/variety -- non-reproductively variation within a subpopulation
      2. Variation/variety -- non-reproductively variation within a subpopulation
      3. Variation/variety -- non-reproductively variation within a subpopulation

Everything yellow would be one kind and the descendants within that kind

Everything orange would be one kind and the descendants within that kind

Everything red would be one kind and the descendants within that kind

Does that help?

Edited by RAZD, : variability instead of viability - thanks Faith


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This message is a reply to:
 Message 130 by Faith, posted 02-15-2014 4:35 PM Faith has responded

Replies to this message:
 Message 134 by Faith, posted 02-15-2014 5:26 PM RAZD has responded
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RAZD
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Posts: 20110
From: the other end of the sidewalk
Joined: 03-14-2004
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(1)
Message 136 of 236 (719599)
02-15-2014 6:12 PM
Reply to: Message 134 by Faith
02-15-2014 5:26 PM


The problem with that system, RAZD, is that while it's technically true enough it blurs the line where you get another Kind from a former Kind, which is still what the ToE claims ...

Once again, evolution does not say that. It is always nested hierarchies, and no evolution at any stage steps outside the hierarchy they come from -- that would in fact counter evolution and falsify evolution.

... . All you are doing is insisting that the change comes about so gradually that one can't identify that line at all, basically trying to define the debate out of existence. ...

Not really sure what you are saying here, but as far as I can see there are two basic differences between evolution and creation:

  1. age of the earth
    • creation happened circa 6,000 (to 12,000 depending on sources) years ago vs
    • scientific data\evidence shows a measured minimum age of 4.5 billion years and

  2. the number of original parent populations
    • creation has a number of fairly advanced created kinds (number unknown, but they filled the ark)
    • scientific data\evidence shows a small number of primitive single cell organisms are most likely the rood source of all life on earth

They are somewhat interlinked -- greater age benefits evolutionist views (makes it more feasible), shorter age benefits creationist views (makes it more feasible).

Another way to look at is the three kinds/clades in Message 133 have a common ancestor by evolutionary views and that they don't have a common ancestor by creationist views.

This leads to a testable prediction: evolution if every group can be linked to any other group via common ancestors as you go back in time with and end in some single cell breeding population; creation if common ancestors cannot be found between groups at a specific fairly recent point in time.

ie -- evolution if the yellow, orange and red clades are found to have a parent common ancestor population that they are each descendant from; creation if there is no parent common ancestor population found.

In one sense this should also be able to tell us how many "kinds" there are by looking at the nested hierarchies (that are predicted by both views) and seeing where the end up in a parent common ancestor that is not descendant from another earlier parent population.

In addition we can test for the flood by looking for a common genetic bottleneck at the time of the ark.


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This message is a reply to:
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RAZD
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Joined: 03-14-2004
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Message 138 of 236 (719604)
02-15-2014 6:41 PM
Reply to: Message 135 by Faith
02-15-2014 5:36 PM


... variability (not "viability"), ...

Ooops I'll fix thanks.

But the problem is you aren't looking for reduction in genetic variability (not "viability"), which is why you have not "seen" it. You are not looking where it would be found. There is no way this is NOT the case. ...

As whole genomes become sequenced and the variations of individuals mapped against a "species standard" genome, there is no way that this variability will NOT be mapped.

As it stands with the current state of genomes there are no locations holding hidden variations sufficient to result in anything more than variation level change that would be expected via evolution views of mutations moving a section of DNA from one location to another -- not enough to change a domestic cat into a tiger or vice-versa ... which of course would be within what is expected of the evolutionary model.

Should we expect anything more from the creationist model?

... When you have a population based on reduced numbers you HAVE to get reduced genetic variability in the population as a whole, ABE: though this may not be apparent until the numbers have been appreciably reduced so that the trend can become apparent. At first you'll just get the usual remix, the new gene frequencies, and new phenotypes from them, but in order to do that you have to reduce the competing alleles, and this only becomes apparent as an overall reduction in alleles as you get further population splits. This COULD be demonstrated in a laboratory. /ABE

Basically what you are saying is that each speciation results in a genetic bottleneck for the subspecies. And that this would be a permanent condition for the subspecies.

And thus we can test for whether

  1. subpopulations after a speciation event have less variation than the parent population, and
  2. the genetic variability stays at a low level after a speciation event.

Would you agree that if the initial cause of reproductive isolation was physical isolation -- say the parent population occupies a peninsula and an earthquake or hurricane causes part of the peninsula to become an island, with a gap that this population cannot cross -- that the population on the remaining peninsula and on the island have the same amount of variation\variability?


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This message is a reply to:
 Message 135 by Faith, posted 02-15-2014 5:36 PM Faith has responded

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 Message 139 by Faith, posted 02-15-2014 7:46 PM RAZD has responded

  
RAZD
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Posts: 20110
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.9


(1)
Message 143 of 236 (719745)
02-17-2014 11:36 AM
Reply to: Message 139 by Faith
02-15-2014 7:46 PM


Re: Predictability of Genetic Variability
The best way to see a trend in the amount of genetic variability would be by comparing genomes from a series of population splits into daughter populations where you know the number of founding individuals and what sort of phenotypic changes came to characterize each population over some known number of generations. I've come to think of the percentage of heterozygosity as the main indicator, and I've thought this could be tested by looking for the percentage of heterozygosity in a series of ring species in the wild, but probably the best test would be in the laboratory where you could control for all the variables.

AND by doing a follow-up study to see if "genetic variability" stays at that level.

Not a bottleneck because that involves a very drastic reduction in numbers for the founding of a new population, and I'm thinking of a more normal-sized founding population. ...

But you only have two members to make up a whole breeding population from the kind\clade on the ark -- you don't\can't have "a more normal-sized founding population. "

... But I AM saying that the trend to [ABE: REDUCED/ABE] genetic variability should be the case in all such population splits anyway, and yes, that it would be a permanent condition for the subspecies barring a reintroduction of gene flow.

So any finding of increased "genetic variability" would invalidate and falsify your hypothesis?

Such as the E.coli increased variability that allowed one group to become citrate consumers while other groups and that group before the new ability was expressed.

No RAZD, not "less VARIATION," but less GENETIC VARIABILITY. There is a big difference. You may be getting much greater variation in the phenotypes, in fact you should, but the genetic variability should also be getting reduced in the process.

Now you are arguing a rather pointless opinion that is rather obviously invalid ... because variability would be the ability to vary -- which is what happens every time offspring are produced, all the indels and point changes that you just can't stop from happening.

... not "less VARIATION," but less GENETIC VARIABILITY. There is a big difference. ...

Indeed: one occurs (less variation) and one doesn't (less variability).

OK. You are of course counting on mutations, ...

Obviously, since they are a fact, they have been observed.

... which of course you expect to be viable mutations ...

Not quite: which of course we expect to be random. Whether or not they are viable is determined by the survival of the offspring to reach the point of further reproduction. Some will, and some won't. Note that somewhere around 75% of human blastocysts (zygotes that have implanted on the uterus wall) are later ejected as non-viable and that the remaining 25% still have mutations. This is observed data, not made up.

... that make real alleles ...

A possibility, but not highly likely from one mutation alone. For instance the E.coli mentioned above required two mutations, where the first one enabled the second to be functional, and subsequent generations from before that first mutation do not evolve the second, but that ones after it are so able. I would expect alleles for multicellular life to be more complicated.

... and occur in the germ cells so they can be passed on. ...

Which is necessary for heredity to occur - and thus of interest to evolution - but not all mutations affect germ cells and thus only affect the organism itself. Those in this later group could affect the development of the organism and it's ability to survive and even to reproduce, but they could not be inherited, and would be lost in the next generation.

Even ones that are in the germ cell can be lost in the next generation if there is failure to reproduce.

... But if such mutations did enter into the picture it should have the same effect as the reintroduction of gene flow from any source: ...

The likelihood of a mutation replacing a lost allele would be extremely low, while the likelihood of a mutation causing or assisting in causing a new allele would be much much higher.

... that is, it would change the new subspecies' phenotypic character into something else. It would in effect be a new "speciation" or subspeciation. ...

Not really, it would cause a new variation, but it would still be carried by a member of the breeding population, and only by selection for survival and reproduction can it be passed on to later generations. It would need to become "popular" within the breeding population before you could have a speciation\subspeciation demarcation of daughter populations.

... "speciation" or subspeciation. ...

btw -- can you tell me (again?) what the difference is between these? Is it a necessary part of the description of the nested hierarchies here? It seems to me potentially confusing.

Are subspecies genetically reproductively isolated daughter populations?

Or physically reproductively isolated daughter populations?

Or not reproductively isolated daughter populations (ie - varieties)?

... But I don't think you'd find any genuine increase in the genetic variability anyway, so OK, yes, that would be a test.

And if we find no decrease in variability is that also a test?

If we find an increase in variation, is that a test? If we find a new variety and can show that it did not exist before ... is that a test?

I'm not sure why HOW the formation of a daughter population should change things. Migration of the new population to a new geographic area would accomplish the same thing, assuming reproductive isolation as well. In any case it depends on the numbers involved. ...

Indeed that would be similar. The difference would be the likelihood of both populations carrying all the then current alleles within their breeding members. This would mean no reduction in the populations without further selection to adapt to the different ecologies (even if they are fairly similar).

So yes it depends on the numbers.

... it should show a reduction in genetic variabilithy, but not right away ...

Why?

... At first if you checked individual genomes they'd have the same genetic variability of course. ...

Agreed. So what changes?

... It would take a few generations for the different gene frequencies in the two populations to show up ...

What changes in the variability?

We would expect some changes in the variations between the two populations as they adapted to the different ecologies, different challenges to survival and breeding. A change in the gene frequencies would be a change in the variations of phenotypes within each breeding population, not in their ability to vary.

... in the development first of many different phenotypes and then a recognizable new phenotypic character for the population as a whole, ...

But you are not saying that the ability to vary is changing, you are saying that the distribution of varieties is changing.

For a new phenotype character to emerge it would either need to be either recessive (rare rather than non-existent in the previous populations), suppressed (by a gene that is lost, either by selection or drift), or new (due to new mutations).

... and that's when I'd expect a reduction in genetic variability to start to become measurable.

And if we find no change in variability does that invalidate your hypothesis?

Curiously, I would expect no change in variability, but I would expect a change in varieties in both populations that are now isolated.


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Rebel American Zen Deist
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This message is a reply to:
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RAZD
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Posts: 20110
From: the other end of the sidewalk
Joined: 03-14-2004
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Message 154 of 236 (719827)
02-18-2014 1:55 PM
Reply to: Message 153 by Taq
02-18-2014 12:20 PM


Faitholution
Her argument is that changes to the human genome can only produce damage. ...

Welcome to Faitholution, where any term used by scientists is suspect because it implies that evolution is true, so she describes actual evolutionary processes but says that the terms are not appropriate ... hence subspecies and variability.

Her argument is that changes to the human genome can only produce damage. ...

Anything beneficial or neutral will be from hidden alleles from the original kind, anything deleterious will be mutations.

The test for that is to see if genomes ...

... show beneficial mutations that are not in previous genomes. Not that it will do any good ...

Edited by RAZD, : ,,,


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RAZD
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Message 157 of 236 (719848)
02-18-2014 5:18 PM
Reply to: Message 156 by Taq
02-18-2014 4:48 PM


Re: Paradigm clash
Odd you would think I or anyone thought otherwise.

"You can't prove that mutations do anything but damage DNA."--Faith

Within each of the kind\clades ... of course she needs to establish the root kind\clade ...


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RAZD
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(1)
Message 233 of 236 (720707)
02-26-2014 6:55 PM
Reply to: Message 225 by Faith
02-26-2014 1:49 PM


Re: Mouse Genetics
To add to what others have said:

How did the mutant allele occur just in time to form a dark population of mice? Mutations ARE random and unpredictable aren't they? Or not? You get this allele JUST IN TIME,

Where just in time is the geological period between the lava flow occurring and the mice mutation occurring, where this could involve thousands of years and generation time is 1 or 2 years.

... one of your arguments that it IS az mutation is the fact that it's dominant, ...

Or that it became dominant in the mice on the lava field due to the suppression of tan mice -- if it started out with the tan allele being dominant then selection would have been strong for DD mice, and thus it could become fixed in those mice.

... Hey by the way how does that ONE germ cell with the mutant allele happen to get passed on anyway?

By mating with a tan mouse.

So for whatever reason that other gene is the one where the rare allele happened to show up in that other population. The rare naturally occurring allele, not a mutation. The odds are far more against mutation than against my scenario.

They are different mutations, different alleles, different changes to the development process of offspring so that dark fur is expressed instead of tan fur.

The odds aren't a LOT better for built in alleles but at least they would already have been in the population ...

Nope: neither of the two mutations are found in the tan mice populations between the two locations.

Melanism is a very common mutation in all species:

http://en.wikipedia.org/wiki/Melanism

quote:
Melanism related to the process of adaptation is called adaptive. Most commonly, dark individuals become fitter to survive and reproduce in their environment as they are better camouflaged. This makes some species less conspicuous to predators, while others, such as black panthers, use it as a foraging advantage during night hunting.[6] Typically, adaptive melanism is heritable: A dominant gene, which is entirely or nearly entirely expressed in the phenotype, is responsible for the excessive amount of melanin.

Even in humans.


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This message is a reply to:
 Message 225 by Faith, posted 02-26-2014 1:49 PM Faith has not yet responded

  
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