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Author Topic:   Introduction to Genetics
JonF
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Posts: 4120
Joined: 06-23-2003
Member Rating: 1.6


Message 226 of 236 (720690)
02-26-2014 2:27 PM
Reply to: Message 225 by Faith
02-26-2014 1:49 PM


Re: Mouse Genetics
.

Edited by JonF, : Submitted too soon


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

  
JonF
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Posts: 4120
Joined: 06-23-2003
Member Rating: 1.6


(2)
Message 227 of 236 (720692)
02-26-2014 2:35 PM
Reply to: Message 225 by Faith
02-26-2014 1:49 PM


Re: Mouse Genetics
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?

Short answer: luck. Luck happens. People win the lottery. Most don't.

If it had not arisen mice wouldn't have moved into the black lava ecosystem. Something else might have. Or the mice might have died out completely if the black lava wiped out the brown desert. All sorts of other scenarios are possible. One scenario happened. Randomly.

Remember that the vast, vast majority of species, estimated well over 90%, did not get a beneficial mutation in time to avoid extinction.

So it pairs with an ll and could make four babies, two lls and two Dls. At best.

Yup. Or maybe four LLs or three LLs and a DL. All the DLs are dark. So what?

And what's to stop this predator that has kept the population light forever from just picking off those two little dark babies as soon as they are born?

Nothing. Luck of the draw.

And what's to stop this predator that has kept the population light forever from just picking off those two little dark babies as soon as they are born?

You have no idea what the probability of any appropriate mutation, the ones discussed or others that might have similar effects, is. Depending on how many different mutations would have the effect and other factors, the odds will still be small but still reasonably possible. Or not. It just doesn't matter. Even if the odds are minuscule, events that are astoundingly improbable happen all the time.

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.

The probability of your scenario, an allele that has persisted for thousands of years against selective pressure, is 0.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000.

The odds are against the whole scenario.

You don't have a glimmer of a clue what the odds are.

Remember, almost all species lose the evolution lottery. Winners are as rare as state lottery winners.


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Taq
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Posts: 7430
Joined: 03-06-2009
Member Rating: 2.5


(1)
Message 228 of 236 (720698)
02-26-2014 4:17 PM
Reply to: Message 225 by Faith
02-26-2014 1:49 PM


Re: Mouse Genetics
How did the mutant allele occur just in time to form a dark population of mice?

The mutation would have been popping up now and again throughout the history of the pocket mice population. The same thing happens with antibiotic resistance in bacteria. The mutation is occuring at a set probabilistic rate. It isn't until you add selection that antibiotic resistance comes to dominate the population.

Experiments like the Luria-Delbruck fluctuation experiment and the Lederberg plate replica experiment demonstrate why it only appears that the mutation shows up in time. The truth of the matter is that the mutation is occuring at the same rate through history, irrespective of if it is beneficial or not.

http://en.wikipedia.org/...%E2%80%93Delbr%C3%BCck_experiment

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169282/

Those are the two classic experiments that still define what biologists mean by random mutation. They might be worth going over if you would be willing to discuss it.

Because it gets passed on. Just when the light mice are getting to the lava field apparently.

I, nor anyone, ever made that claim. It only had to happen in a population near the lava fields sometime after the eruptions. Could have been 10,000 years after the eruption, or 100,000. Could have happened 500,000 years after the eruption, and just a few thousand years before humans moved into the area.

It's a Dl, it will have to pair with an ll.

Ever use a Punnet square?

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

In this case, offspring from Dl ll parents will have a 50% chance of being dark because D is dominant over l.

And what's to stop this predator that has kept the population light forever from just picking off those two little dark babies as soon as they are born?

Nothing. The gene could have appeared and disappeared multiple times. Doesn't change the fact that it did survive and was passed on at some point, and in two lava fields to boot.

As you say there is apparently more than one gene that can mutate to make dark fur color. The problem is that the odds are against this happening for starters, just in time for the lava field, then they are against the offspring surviving assuming they get produced, then they are against them growing up to make more dark mice.

Yes, there are at least two gene loci where mutations can produce dark fur, and probably more than two.

I will also look forward to seeing your probability calculations that show why this is improbable. You will be showing us those calculations, won't you? You wouldn't just claim that it is improbable without anything to back it up, would you?

The odds aren't a LOT better for built in alleles . . .

What built in alleles? Evidence please.

Edited by Taq, : No reason given.


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New Cat's Eye
Inactive Member


Message 229 of 236 (720700)
02-26-2014 4:26 PM
Reply to: Message 225 by Faith
02-26-2014 1:49 PM


Re: Mouse Genetics
How did the mutant allele occur just in time to form a dark population of mice?

It didn't occur just in time. It happens all the time. Its just that when a black mouse pops up in a light colored environment, it can't hide and gets eaten right away (so the gene doesn't spread).

But when there is a dark environment, those black mice that pop up every now and then can now hide better than the other mice, so the other mice get eaten instead of them and the gene gets passed on.


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Replies to this message:
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Faith
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Posts: 28070
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 230 of 236 (720701)
02-26-2014 4:50 PM
Reply to: Message 229 by New Cat's Eye
02-26-2014 4:26 PM


Re: Mouse Genetics
The problem with that argument is that it justifies my claim that it wasn't a mutation but a regularly occurring allele. It would have to keep recurring after all for your scenario to be true and not just be eliminated completely by the predator. But Taq insisted that it had to be a mutation because it's dominant, meaning that there had been NO allele for black fur in the population earlier, so it had to have occurred just in time for the selection. An earlier mutation would have put it in circulation just as a regularly occurring allele would have. That particular argument by Taq that it's a mutation from its dominance therefore no longer applies.
This message is a reply to:
 Message 229 by New Cat's Eye, posted 02-26-2014 4:26 PM New Cat's Eye has responded

Replies to this message:
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Taq
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Posts: 7430
Joined: 03-06-2009
Member Rating: 2.5


(1)
Message 231 of 236 (720702)
02-26-2014 4:57 PM
Reply to: Message 230 by Faith
02-26-2014 4:50 PM


Re: Mouse Genetics
The problem with that argument is that it justifies my claim that it wasn't a mutation but a regularly occurring allele.

It would have been removed from the population by negative selection, so that explanation is out.

But Taq insisted that it had to be a mutation because it's dominant, meaning that there had been NO allele for black fur in the population earlier, so it had to have occurred just in time for the selection.

Where did I say that it had to happen "just in time for the selection"? I never said any such thing.

An earlier mutation would have put it in circulation just as a regularly occurring allele would have.

It couldn't circulate because of negative selection.

That particular argument by Taq that it's a mutation from its dominance therefore no longer applies.

It most certainly applies, as does the lack of sequence variance in the dark allele compared to the light allele. On top of that, the regional differences for dark color adaptations is the cherry on the Sundae.


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New Cat's Eye
Inactive Member


Message 232 of 236 (720705)
02-26-2014 5:23 PM
Reply to: Message 230 by Faith
02-26-2014 4:50 PM


Re: Mouse Genetics
The problem with that argument is that it justifies my claim that it wasn't a mutation but a regularly occurring allele.

Not necessarily. It could be similiar mutations occuring at different times, or it could be a different mutation causing a similiar change in fur color.

There's more than one way to get a black mouse.

It would have to keep recurring after all for your scenario to be true and not just be eliminated completely by the predator.

No it gets completely eliminated and then later another different black mouse pops up again. And then it gets eliminated. Then another different one pops up, but wait... this time he ends up in a dark colored environment. So he thrives and passes the gene on. It could be a different mutation than the earlier ones that didn't make it.


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 Message 230 by Faith, posted 02-26-2014 4:50 PM Faith has not yet responded

  
RAZD
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Posts: 19484
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.5


(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:
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Faith
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Posts: 28070
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 234 of 236 (833183)
05-18-2018 11:01 AM


Picturing DNA as related to phenotypes and diseases
I've been reading up on some basic information about genetics among other things and realized I have a very fuzzy idea of how various familiar concepts relate to the DNA molecule. For instance reading about genetic diseases I found out that a mutation in a "single gene" or "single copy of a gene" usually doesn't cause disease, that disease usually (though not always) manifests only when two copies of a gene have the same mutation (meaning one copy got inherited from each parent.)

Does "two copies" refer to the two sides of the DNA strand? Is there a "sidedness" to the strand? Is there a way to recognize a recessive versus a dominant gene by the appearance of the DNA double helix itself? The chemicals on each side are complementary to each other, not identical (the T, G, A, C). Does that have anything to do with this?

Sorry if I'm being obtuse. But of course that won't surprise anyone here.

This question got started on the subject of color blindness, which one site says IIRC requires two copies of the recessive mutant gene to manifest. I can find the site if necessary. So when they say the mutation occurred in a "single gene" they mean one side of the pair that makes up the double helix? Are there particular distinguishing features to each side or strand?

And this raises a question about recessive versus dominant. You can have either a BB for brown eyes or a bb for blue eyes or the heterozygous Bb that also produces brown eyes. So are we talking about the two DNA sides here and does it make sense to say "homozygous recessive" and "homozygous dominant" or what?

I also found it interesting that the site said mutations can cause either missing or deformed proteins.

The relation of proteins to phenotype is very mysterious. Any comment on that?

Thanks to anyone who can straighten me out about these questions.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


Replies to this message:
 Message 235 by Taq, posted 05-18-2018 4:08 PM Faith has responded

    
Taq
Member
Posts: 7430
Joined: 03-06-2009
Member Rating: 2.5


Message 235 of 236 (833235)
05-18-2018 4:08 PM
Reply to: Message 234 by Faith
05-18-2018 11:01 AM


Re: Picturing DNA as related to phenotypes and diseases
I may quote your previous post out of order so that my explanations will make more sense.

Faith writes:

Does "two copies" refer to the two sides of the DNA strand?

No. The "two copies" refers to two separate chromosomes in a chromosome pair. Complementary DNA is the DNA on the other strand while alleles are copies of a gene found on separate chromosomes. You get one chromosome of each pair from each parent so that you have two alleles for each gene. This is what the chromosomes look like in the nucleus of human cells:

An allele is the copy of a specific gene found on each of those paired chromosomes.

Is there a "sidedness" to the strand?

Yes. The "direction" of each strand is determined by the carbons in its sugar backbone. DNA is copied and transcribed in what is called the 5' to 3' direction. DNA sequences are often written with the 5' and 3' designations, especially when showing double stranded DNA. For example:


5'--ATATTCGCATT--3'
3'--TATAAGCGTAA--5'

If you write a DNA sequence without the 5' and 3' designations then it is assumed the first letter is on the 5' side.

There are youtube videos on the subject if you are interested:

https://www.youtube.com/watch?v=IV53GZGr11g

It is also important to note that the two strands go in opposite direction, and genes can be found on either strand throughout a chromosome. The strands are arbitrarily labeled the + or - strand.

For instance reading about genetic diseases I found out that a mutation in a "single gene" or "single copy of a gene" usually doesn't cause disease, that disease usually (though not always) manifests only when two copies of a gene have the same mutation (meaning one copy got inherited from each parent.)

In general that is true. If one allele produces a non-functional protein while the other allele produces a functional protein the functioning allele can usually make up for the non-functional one. If you have two copies of the recessive non-functional allele then you may have problems.

However, a mutation in one allele can produce a protein that causes disease all on its own which a non-disease allele can not make up for. This is the case with achondroplasia (aka dwarfism) where having just one allele can cause dwarfism and having two disease alleles results in a nonviable embryo. You can also have alleles that are equally functional, as in the case of blood types.

Is there a way to recognize a recessive versus a dominant gene by the appearance of the DNA double helix itself?

Not to any great extent. It is very difficult to know if a mutation is going to produce non-functional protein that is also non-detrimental, a protein with the same function, a protein with a different function that combines with the other allele in an equal fashion, or a mutation that results in a protein that causes disease all on its own.

And this raises a question about recessive versus dominant. You can have either a BB for brown eyes or a bb for blue eyes or the heterozygous Bb that also produces brown eyes. So are we talking about the two DNA sides here and does it make sense to say "homozygous recessive" and "homozygous dominant" or what?

If you have two copies of the same allele then you are homozygous. If you have two copies of different alleles then you are heterozygous. BB and bb are homozygous while Bb is heterozygous.

I also found it interesting that the site said mutations can cause either missing or deformed proteins.

Mutations can also result in proteins with different functions or the same function. For example, if you compare the cytochrome C gene found in humans with the same gene in yeast you will find that they differ by 40% yet they still function in the same way.


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 Message 234 by Faith, posted 05-18-2018 11:01 AM Faith has responded

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Faith
Member
Posts: 28070
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 236 of 236 (833292)
05-19-2018 10:47 AM
Reply to: Message 235 by Taq
05-18-2018 4:08 PM


Re: Picturing DNA as related to phenotypes and diseases
Thank you, I've copied that into a Word document to ponder it further. I see I now need to ponder the relationship between the chromosome and the DNA strand. Yes I'll be watching the videos.
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