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Author Topic:   Introduction to Genetics
Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 208 of 236 (720072)
02-20-2014 4:28 AM
Reply to: Message 206 by saab93f
02-20-2014 1:46 AM


Re: Paradigm clash
It is just that you propose creationists "models" or "theories" when in fact they do not exist. Everything creationism has accomplished so far is to say that ToE is wrong without giving an alternative that has some sort of explanatory power.

Science works in exactly that way that new ideas are brought to the fray and then scrutinized using the scientific method.

We can both repeat our complaints about our opponents' point of view, plus you've added the usual Science Creed and the Evo Creed, and it's all simply a statement of belief.

I can understand that it is particularly offensive even to consider that creationists DO have a point of view that should be taken seriously, because you are so convinced that it is science that you are defending, against what you think of as religion.

Creationism begins with assumptions and distorts evidence thus it NEVER can produce anything viable.

Just to make it clear, there is NO creationist model or theory, just denial of evidence.

All you are doing here is a tit for tat, echoing exactly what I've been saying about evolutionism. Of course I suppose it can be said on both sides, but it IS true of evolutionism as I've been pointing out, that the interpretive sciences that support the ToE are wrapped around bald assumptions without any verification whatever. I believe I've shown this many times.

I disagree of course that creationism "distorts" anything. We explain the same evidence that you explain, but explain it differently. The evidence is not distorted in the process, simply differently interpreted.

And of course I disagree with every word you've said anyway. I have been presenting, albeit in bits and pieces, what should be considered to be at least a creationist model in the making. It does have explanatory power, you just don't like the explanation. And of course you could say the same thing about my opinion of evolutionism. Is there any point in continuing to state and restate these obvious opinions?

  • The ToE says All life was descended from earlier life. This is an article of faith, of belief, based on commitment to the ToE. It hasn't been shown to be true and it can't be shown to be true (is this a better way of saying it than "proved?) The particular Creationist model I've been pursuing says all life was created as separate Species in the same time frame as human beings. This IS a different model, wouldn't you say?

  • THe ToE says DNA evolved just as everything else did; YEC as I've been pursuing it says DNA was built in to the original Species or Kinds and the genome of each governs only that Species, and again, surely this must be considered to be an alternative model.
    --- My particular defense of this idea is that the processes of evolution that isolate populations from each other, which is the general way races are formed, lead to reduced genetic diversity. This also appears to be the main route to "speciation" but if the supposed "new species" in fact has reduced genetic variability this is clearly a wishful fantasy. The YEC model as I understand it says that life was created to vary, to evolve over time, into myriads of fascinating new races, but that a calamity known as the Fall brought death into the world and now all life is threatened by disease and death whereas if the Fall had never happened we'd just have beautiful subspecies of every known Species. And again, this IS a model and it does have explanatory power. It's obvious that species are threatened by extinction. That's why we have conservationist programs.

  • The ToE says that mutations are the means by which DNA was/is created, while also admitting that most mutations are neutral and many are deleterious, claiming the latter are selected out. My YEC view says this is a complete misunderstanding, that mutations are not a normal occurrence, or let's say most of them aren't, they are mistakes, and their overall effect is destructive, even though this may not show up for quite some time. There ARE, however, thousands of known genetic diseases, and only a tiny number of mutations that are even claimed to confer any known benefit, and in most cases the benefit is a trade-off with another disease, such as malaria protection by sickle cell anemia. This looks like a thoroughly inadequate method for producing viable genetic material. And again, this is a plank in a creationist model. The facts fit the model of life's actually deteriorating rather than improving in any way.

  • The ToE also proposes of course that mutations make up for any reduction in genetic diversity. My YEC model says 1) mutations hardly ever IF ever make DNA that acts like normal functioning DNA. The best it can do is manage not to change things, but then what do you have? Nothing really. And 2) if mutations did add genetic diversity of a valid kind to a new population, all they could add is an allele to replace another allele and one or the other is going to get selected to make up the overall "look" of the population and in the end since one gets selected out there is nothing that can really be called an increase in genetic diversity.

  • The ToE says evolution has created everything that now lives and that this has been going on for many millions of years. The evidence for this is all circumstantial, basically boiling down to the observation of similarities with differences between organisms that can be arranged in a mental hierarchy. This gets translated into Genetic Descent with Modification although this is nothing more than a definitional coup without anything in actual reality to corroborate it. This is in fact only Reification: the treating as real of a mere mental construct or theory, calling it Fact when it's only word manipulation. YEC of course says the original Species are confined to their own genome, which has the capacity to vary enormously but always within the genome, always within the Kind. This IS a model, and it does account for the known facts.

  • The ToE's evidence includes the fossil record which is remarkably sorted from bottom to top according to what seems to be a hierarchy of development from more primitive to more advanced or modern (certainly complexity is not the criterion since the "lower" creatures are often amazingly complex). Of course one could wonder why evolution would operate in any particular identifiable direction onwards and upwards since one of its cardinal "tenets" is "fitness" which shouldn't imply any particular direction of adaptive traits, but it does have to be admitted that it LOOKS plausible if you allow for that idea and it seems to defeat the YEC idea that the worldwide Flood of Noah explains all the strata and their fossil contents. Nevertheless the Flood does remain the YEC alternative model to the Geologic Column, and it does have explanatory power.

Well, that's a few elements of the debate as I see it, including both the critique of the ToE and the alternative model that opposes it, just off the top of my head. I'm sure I've left a lot out, but it looks to me like there is both a critique of the ToE AND an actual model on the YEC side that opposes the evolutionist model, and that your objections are false.


This message is a reply to:
 Message 206 by saab93f, posted 02-20-2014 1:46 AM saab93f has seen this message

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Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 215 of 236 (720139)
02-20-2014 12:15 PM
Reply to: Message 214 by Coyote
02-20-2014 10:58 AM


Re: Just some examples of assumptive mystification versus genuine science
I've answered you about the word "proof," that I think it's just a way to rationalize pretending that evolution is scientific in the same sense that the hard sciences are. If you disallow the idea of "proof" you also disallow that distinction. You apparently haven't read anything I said in answer to you about that. But if you are going to insist, I can use other terms like "verification," or "validation" or "confirmation."

Edited by Faith, : No reason given.


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Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 218 of 236 (720162)
02-20-2014 3:15 PM
Reply to: Message 216 by Taq
02-20-2014 12:46 PM


Re: Just some examples of assumptive mystification versus genuine science
So you all say.

Against the evidence, however.


This message is a reply to:
 Message 216 by Taq, posted 02-20-2014 12:46 PM Taq has replied

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Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 220 of 236 (720200)
02-20-2014 7:52 PM
Reply to: Message 219 by Taq
02-20-2014 3:48 PM


Re: Just some examples of assumptive mystification versus genuine science
The evidence of the ERVs was undecipherable, so I asked if you'd please put it into your own words.

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 Message 219 by Taq, posted 02-20-2014 3:48 PM Taq has replied

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 Message 221 by Taq, posted 02-21-2014 11:00 AM Faith has replied

  
Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 222 of 236 (720649)
02-25-2014 11:08 PM


Mouse Genetics
Taq: I'm bringing our discussion of the pocket mice and related issues from the ecology thread to this thread where maybe we can get into some of the general genetics questions and relieve RAZD of an unwelcome subtopic.

As usual, all you are doing is ASSERTING that mutations are the cause of genetic changes.

[Taq] We OBSERVE that mutations are the cause of genetic changes.

Funny then that all you've done is declare it rhater than show such observations.

The evidence does not prove that mutation caused any of it, such as the blackness of the pocket mice. All that is necessary is that a normally-occurring recessive allele become paired up [abe]: and prolific in the population under selection pressure, and perhaps there are other genetic routes to the same result, but mutation does not have to be one of them.

[Taq] The black allele is a dominant trait. You would know that if you had read the paper that I referenced.

Well, this topic has come up before and I vaguely remember that fact anyway. But this fact doesn't necessarily end the discussion. Fur color is one of those traits that is often governed by more than one gene and when that is the case the pattern of dominant-recessive at one gene may not be the dominating influence. I'm not sure how this works, but maybe we could discuss it here.

I did find a couple of links that may or may not be relevant. One is about Rock Pocket Mice but it mostly describes the traits themselves, the "light" type and the "dark" type, and doesn't get much into the underlying genetics, though it does mention that both dominant and recessive alleles are maintained in a population.

The other is about general Mouse Genetics and it shows that black and white parents produce many "agouti" colored offspring. Black is dominant and white doesn't occur until a black is paired with an agouti.

It isn't said but the very existence of the agouti suggests that more than one gene is involved.

This is for black and white not "light" and "dark" and I'm not sure whether we're talking about two different genetic pictures or if the same principles apply, but if it's the same situation the hard thing to explain would be the light mice rather than the dark, because they would be recessive and if only one gene governs the color it would have to be paired to produce it. But if the statement from the first link is correct that both dominant and recessive alleles remain in the population then we can assume that the alleles for dark are in the light population. The D for dark would be rare in the population but you could still get a combination of Dl with ll which would most often always produce the light type, and also even the occasional Dl with Dl which would produce the light type half the time.

Then what happened when the dark were selected for the lava area would have been the favoring of the DD type and the loss of the ll type. If other genes are involved, however, there could be other factors that produce the light (or dark) even more often. I may not have the clearest grasp of how all this works but that's one reason I brought it to this thread.

Also, the black lava is much younger than the desert that surrounds it. The black allele is strongly selected against in the light colored desert to the point that even the dominant black allele can not be found in populations found any decent distance away from the black lava fields.

This is not the case of a recessive gene becoming prominant. It is dominant, and it doesn't exist in the light colored population,

How do you know this? It could be rare rather than nonexistent.

and would not have existed for any appreciable time before the appearance of these black lava islands. The genetic evidence clearly shows that it is the emergence of a mutant allele in the recent past.

The fact that the dark allele didn't show up very often in the population isn't proof that it wasn't there, it was merely selected against.

======================================================
[ABE]: All the above is not completely satisfactory and I've been thinking more about it. If you get a mutation, this one dark allele, you are also getting a dark colored mouse right away if it's passed on because this allele is dominant. So you've got, what, one or a few dark mice in a litter or what? And where is this occurring? Is it occurring in the light population or have some of the light colored mice ventured onto the lava already so the dark mice are born there or what? You are going to have to have some mice exposed to predators whether the dark ones in the light population or the light ones against the lava.

Is that one mutation enough to produce the new population of dark mice? It's possible I guess. Since it's dominant you'd have a Dl individual with the mutation plus ll so you could easily get a couple of Dls in the next generation, both of course dark mice. If they are in the light colored population and manage to survive they may produce some more Dls in the next generation and by the third and fourth some DDs as well.

But again, one way or another one of the colors is going to be vulernable to being selected out by predators.

That being the case, this really isn't a strong argument for mutation at all, but for the rare occurrence of a normally occurring D in the population from time to time. When the selection pressure occurs it would be when some of the light population have ventured onto the lava with a few darks among them. The lights get picked off and the darks go on to multiply.

One way or another you are going to have to have a few darks among the lights and a few lights among the darks and that's only really likely to happen for purposes of selection if both are already present in the population. [/ABE]

====================================================

Or perhaps you can tell us why the observed mechanisms of mutation could not produce the black allele.

[ABE]: After writing the above "ABE," I see that one argument against mutation is that a single dark allele is going to produce maybe a couple of dark baby mice which would expose them to predators whereas a regularly occurring dark allele already in the population would be producing dark babies from time to time anyway, and the chances for their survival are greater than the one mutation's chances. So I conclude that there's really no good argument for mutation as the source of the dark type. [/ABE]

Well, the observed mechanisms of mutation are usually described as mistakes, and the various ways they occur certainly look to me like mistakes and nothing I'd expect to happen *normally* to the amazingly complex and incredibly well organized DNA system.

Plus the fact that you all acknowledge that mutations are the cause of an amazing number of genetic diseases, not ALL of which are "selected out" by the way although that is the accepted wisdom. I just saw an article about a very rare genetic disease that two brothers didn't know they had until adulthood when now their lives are threatened by something they didn't even know they had, this Alport syndrome.

PLUS all those "neutral" mutations which are observed, which as far as you know do nothing, which is rather odd, again, in such an incredibly complex and amazingly organized genetic system.

PLUS the fact that you really don't KNOW of many clearcut beneifts of mutations, and even those you can point to are rather iffy.

PLUS the fact that the mutation would have to occur specifically at the gene for fur color in time to produce the favored dark mouse and occur in mice that have ventured onto the lava field rather than in the light mice where it would only be selected against. What are the odds?

Plus the fact that it would have to produce the right sequence so as not to mess up the fur color gene completely. Maybe that's not too hard since a "neutral" mutation wouldn't change much anyway, but then wouldn't we expect just another "light" to show up? How is it going to produce enough of a change to produce a dark over a light? Odds again seem to be a problem here.

There are a few reasons for you.

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Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 223 of 236 (720652)
02-25-2014 11:37 PM
Reply to: Message 221 by Taq
02-21-2014 11:00 AM


retrovirus
Thanks for the info about the retrovirus. I may have some questions later.

Edited by Faith, : No reason given.


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Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 225 of 236 (720687)
02-26-2014 1:49 PM
Reply to: Message 224 by Taq
02-26-2014 11:30 AM


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? You get this allele JUST IN TIME, see, because one of your arguments that it IS az mutation is the fact that it's dominant, so the idea is that the population previously had NO allleles for dark fur. Now it has one. It occurs in the germ cell, right? Because it gets passed on. Just when the light mice are getting to the lava field apparently. So it gets passed on. It's a Dl, it will have to pair with an ll. Hey by the way how does that ONE germ cell with the mutant allele happen to get passed on anyway?

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

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? Or is this happening on the lava field? If so, how is the light one managing to escape the predators long enough to produce the babies?.

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.

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 odds aren't a LOT better for built in alleles but at least they would already have been in the population and showing up from time to time so we don't have to count on luck to produce them at precisely the right moment. And it WOULD be luck, right? So far nobody has said that mutations show up exactly where there are needed when they are needed, they ARE a random "mistake," or are they not?

In the case of built in alleles they'd show up just as occasionally on the lava as they did on the sand, but there they'd be selected for. But wouldn't we expect a mutation to show up in the light population on the sand? Or is that mutation just SO precocious that it waits to show up on the lava?

I don't find your arguments for mutations to be convincing. The odds are against the whole scenario. OK, I'll read your post again and think about it more but one read through still says there is no way to be sure those are mutations.


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Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


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.

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Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


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.

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Edited by Faith, : No reason given.


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 Message 235 by Taq, posted 05-18-2018 4:08 PM Faith has replied

  
Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


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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