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Author Topic:   Introduction to Genetics
Taq
Member
Posts: 6644
Joined: 03-06-2009
Member Rating: 4.1


(1)
Message 166 of 233 (719889)
02-19-2014 1:08 AM
Reply to: Message 164 by Faith
02-19-2014 1:04 AM


Re: Paradigm clash
Not in the absurd sense you were implying.

The "absurd" things I am talking about is how reality works.

However, there is an amazingly long list of genetic diseases and they do take their toll. The fact that such diseases are selected against is itself a toll on the human race for that matter, being the cause of death.

The appearance of genetic diseases due to new mutations is a tiny, tiny percentage of all mutations that occur. That is what you keep ignoring.

However, since I regard them as a disease process in themselves,

Again, we are talking about reality, not the fantasy world that only exists in your head.

Give us evidence, not beliefs.


This message is a reply to:
 Message 164 by Faith, posted 02-19-2014 1:04 AM Faith has responded

Replies to this message:
 Message 168 by Faith, posted 02-19-2014 1:10 AM Taq has not yet responded

  
Taq
Member
Posts: 6644
Joined: 03-06-2009
Member Rating: 4.1


Message 167 of 233 (719890)
02-19-2014 1:09 AM
Reply to: Message 165 by Faith
02-19-2014 1:07 AM


Re: Paradigm clash
The evidence is really mostly in what I hear from you all, about the LACK of evidence for beneficial mutations,

I am showing you that evidence. Among the 40 million mutations that separate humans and chimps are beneficial mutations that are responsible for the beneficial adaptations seen in both species. They are right there.


This message is a reply to:
 Message 165 by Faith, posted 02-19-2014 1:07 AM Faith has responded

Replies to this message:
 Message 169 by Faith, posted 02-19-2014 1:10 AM Taq has responded
 Message 170 by Faith, posted 02-19-2014 1:13 AM Taq has not yet responded

  
Faith
Member
Posts: 25331
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 168 of 233 (719891)
02-19-2014 1:10 AM
Reply to: Message 166 by Taq
02-19-2014 1:08 AM


Re: Paradigm clash
I meant your original absurd statement of what you thought I was saying, which unfortunately I've now forgotten, something about animal DNA, sorry, forgot.
This message is a reply to:
 Message 166 by Taq, posted 02-19-2014 1:08 AM Taq has not yet responded

    
Faith
Member
Posts: 25331
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 169 of 233 (719892)
02-19-2014 1:10 AM
Reply to: Message 167 by Taq
02-19-2014 1:09 AM


Re: Paradigm clash
Shown me? Where?
This message is a reply to:
 Message 167 by Taq, posted 02-19-2014 1:09 AM Taq has responded

Replies to this message:
 Message 176 by Taq, posted 02-19-2014 10:56 AM Faith has not yet responded

    
Faith
Member
Posts: 25331
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 170 of 233 (719893)
02-19-2014 1:13 AM
Reply to: Message 167 by Taq
02-19-2014 1:09 AM


Re: Paradigm clash
I am showing you that evidence. Among the 40 million mutations that separate humans and chimps are beneficial mutations that are responsible for the beneficial adaptations seen in both species. They are right there.

I believe you are simply CALLING normal functioning alleles "mutations." You are not giving evidence that that is actually what they are, this supposedl reality you keep claiming it is. It's just the usual word game, the definitional "evidence" of the ToE which isn't evidence at all.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 167 by Taq, posted 02-19-2014 1:09 AM Taq has not yet responded

Replies to this message:
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Faith
Member
Posts: 25331
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 171 of 233 (719897)
02-19-2014 6:33 AM
Reply to: Message 142 by herebedragons
02-17-2014 9:53 AM


Re: Factual versus interpretive tendentious terminology
Yes, of course. There's the Kind and then there are subspecies or variations on the Kind.

I realize this is your premise, but it is going to cause a lot of confusion to rewrite taxonomic classifications.

Well I don't kid myself that anybody is going to accept my view of things to the point that there would be any need to rewrite anything. That would only happen if this creationist view were recognized as true. How soon you think that's going to come about?

It doesn't make sense to call the red fox, domestic dog, and crab-eating fox subspecies of the original created kind (we can call it Canidae originalis ). [ABE]or to have subspecies of subspecies[/ABE] Classifications are for human convenience to facilitate discussion. Grouping organisms into classifications help us better understand what we are talking about.

I don't know what all is part of a Kind though. I don't see any need to rename anything until that is known.

If you agree that there was an original "ark kind" which then split into two daughter populations, which split again into four daughter populations, etc ... , you will be able to develop a branching cladogram that will look something like this: [chart]You may disagree with the arrangement, but you agree with the basic premise; that the members of the dog kind originated from a common ancestral group, Canidae originalis. Maybe you could propose a very general idea of how you think a tree would look like in you scenario. For example, I would think that the domestic dog would need to branch off very, very early since they have been part of recorded history for many, many years and have undergone heavy breeding. (also keep in mind that the tree shown doesn't include extinct species that are included in Canidae). Then we can apply some tests to your hypothesis to see how well the data supports it.

This just doesn't reflect the way I think about any of this so I don't know what tests could possibly apply. I wouldn't make charts because I don't know what all is in any particular Kind. The chart may have that right or it may not.

Also I don't know of course how the Ark pairs branched off after the Flood. Perhaps many of them ran off to some distance right away, or maybe they stayed around because there was still food available from the Ark for them. As the plant life recovered the animals would have branched out. Predators would have followed the prey. Then their populations multiplied, then after a few generations we get some population splits. All of them go on reproducing, including the original pair; more generations pass, more population splits. Pack animals and herd animals may not undergo as many population splits as, say, cats and bears do. The result of all this is unknowable and uncharitable. I don't see how any tests based on such things would reflect anything I've said.

But if just one allele didn't make it into the new population that's a decrease, and that's very likely to happen with population splits.

A loss of a single allele is not likely to bring about a new subspecies. The situation would be much more complicated than that and require much more significant differences.

You are completely missing my point. The point is that any population is going to bring about a change in gene frequencies, a greater percentage f some alleles, a lower percentage of others by comparison with the original population. This is bound to change the phenotypes in the new group, possibly also the original, depends on the numbers involved. Im trying to make the point that the overall trend will always be to decreased genetic variability, but sometimes all the alleles from the original group will come over to the daughter group and then you don't have that decrease. You DO have new gene frequencies so you DO have new phenotypes if that daughter population remains reproductively isolated over some generations. My point was that you CAN'T have an increase in genetic variability from a population split, but although you might not have a decrease either, you COULD have a decrease, and the loss of even one allele would be a decrease. It's possible there could be a loss of more than one allele. Then if very few of a certain allele come over, eventually that one too could be lost. The point, again, is that the TREND is to a decrease, not an increase. That's the whole point: even the loss of one allele demonstrates the trend.

As long as there is reproductive isolation the only thing that could increase the diversity is beneficial mutations within the new population, and even everybody here agrees that they occur at such a slow rate it would take a very long time for that to make a difference.

But the new gene frequencies themselves should bring about recognizable change within the first few generations.

I wonder, do you think that two identical populations, if kept geographically isolated could eventually be recognized as separate subspecies? What would be the factors that would bring about that change?

Identical in numbers? Like one population splits into two of exactly the same number of individuals? Yes, that is really my argument although I'm usually imagining a daughter population starting with fewer individuals, but even an equal split is going to produce a completely new subspecies given enough generations in reproductive isolation -- because any split is going to change gene/allele frequencies so that there is a greater percentage of some alleles and a lower percentage of others. Both of the new populations should get a completely new mix by comparison with the original population, it would be very unusual if the same mix was retained. THIS is what would bring about the change you are asking about. That's all it takes, the reproductive isolation of a new population with its new allele frequencies.

avoid the implication that the Kind can evolve or vary in any way outside the Kind.

qWe can focus on diversification within the kind.

That's all I'm ever talking about.

In order for your hypothesis to gain acceptance you not only need to show evidence that supports it, but you also need to describe what evidence would falsify it.

I've described the laboratory tests I think would do that job. Or the test of sampling the DNA from each of a series of ring species.

You also need to describe what predictions could be made using this hypothesis. For example, you should be able to arrange all extant canids in a hierarchical pattern based on number of alleles, heterogeneity, number of genes, or some combination of genetic traits.

This doesn't fit with my thinking about this.

In short, develop a model that explains the data better than the current one.

I'd be content for starters if I could just get across this basic scenario I keep describing.

HBD

By the way, on one level I agree with you that population splits can and do reduce genetic diversity, what I disagree with is that it is the whole story.

My argument is that it's the general TREND of all evolutionary processes. But there are of course many different angles that could be pursued.


This message is a reply to:
 Message 142 by herebedragons, posted 02-17-2014 9:53 AM herebedragons has responded

Replies to this message:
 Message 173 by herebedragons, posted 02-19-2014 8:34 AM Faith has not yet responded
 Message 177 by Taq, posted 02-19-2014 11:04 AM Faith has responded

    
saab93f
Member (Idle past 156 days)
Posts: 265
From: Finland
Joined: 12-17-2009


(1)
Message 172 of 233 (719902)
02-19-2014 8:00 AM
Reply to: Message 170 by Faith
02-19-2014 1:13 AM


Re: Paradigm clash
I believe you are simply CALLING normal functioning alleles "mutations." You are not giving evidence that that is actually what they are, this supposedl reality you keep claiming it is. It's just the usual word game, the definitional "evidence" of the ToE which isn't evidence at all.

Mrs Know-it-All. Have you ever thought that the people who have actually studied genetics might know more about it than you AND that they do not have an underlying agenda. You OTOH have an preconception that the Bible is true and are willing to distort anything and everything to conform to it.

I have to gieve you credit that you have read quite a lot - enough at least that you can write stuff that almost sounds scientific. That is more that can be said of most cretins. That does not mean that there was an ounce of honesty or reality or truthfulness in anything you´ve wrote.

Scientists have a very good grasp on how DNA works and how everything we see in reality supports the ToE very nicely. They have not been brainwashed but adhere to the scientific method in which evidence leads to deduction, hypothesis and theories.


This message is a reply to:
 Message 170 by Faith, posted 02-19-2014 1:13 AM Faith has responded

Replies to this message:
 Message 189 by Faith, posted 02-19-2014 4:26 PM saab93f has responded

  
herebedragons
Member
Posts: 1328
From: Michigan
Joined: 11-22-2009
Member Rating: 5.9


Message 173 of 233 (719904)
02-19-2014 8:34 AM
Reply to: Message 171 by Faith
02-19-2014 6:33 AM


Re: Factual versus interpretive tendentious terminology
Well I don't kid myself that anybody is going to accept my view of things to the point that there would be any need to rewrite anything. That would only happen if this creationist view were recognized as true. How soon you think that's going to come about?

Yes, Faith, some will hold on to the ToE as religiously as you hold on to a literal 6 day creation and a global flood and no matter how right you are they will disagree. But the vast majority of us accept the ToE because it is the BEST model we have that can explain the diversity of life. I know it has some flaws, but there is no other model that has been presented that even comes close. If someone presents a model that works better, most of us would adopt it. However, at this point, to get the global scientific community to drastically change paradigms, the evidence would need to be overwhelming, undeniable.

I don't know what all is part of a Kind though.

A major problem for your model. Without a clear and objective way of determining what a "kind" is and what organisms should be included, there is no way to test the model.

Obviously (or maybe not so obviously), a "kind" should be defined as "all organisms, extinct as well as extant, that have diverged through microevolutionary changes from a common ancestral pair (or pairs) that had survived the great flood by being sheltered on the ark."

This definition would generate a branching pattern much like current cladistic analysis do. In fact, unless a different method of generating hierarchical trees is proposed, the trees will look exactly the same. The problem only comes in when the connection is made between "kinds."

This just doesn't reflect the way I think about any of this so I don't know what tests could possibly apply.

I don't see how your proposed model would not generate some kind of hierarchical tree. All these currently living species came from a single mating pair, it would certainly create a branching dendrogram, just like you could trace your family history through a dendrogram.

What is it you object to?

You also need to describe what predictions could be made using this hypothesis. For example, you should be able to arrange all extant canids in a hierarchical pattern based on number of alleles, heterogeneity, number of genes, or some combination of genetic traits.

This doesn't fit with my thinking about this.

So what does? How would you propose to arrange the dendrogram of the "dog kind?" What criteria would you use to determine if two species were closely related or more distantly related (within the kind, of course)?

I'd be content for starters if I could just get across this basic scenario I keep describing. ....

My argument is that it's the general TREND of all evolutionary processes.

I get what your argument is. What I am trying to explore is whether there is anything to your argument. As I said, on one level you are right, any population split will produce two sub-populations with less genetic diversity (or at most equal but never more). So, can we build a model where the reduction of genetic diversity and shuffling of alleles can account for ALL diversification? Can that model be tested against observable evidence and find support?

You have made an observation (population splits result in reduced genetic diversity) and created an hypothesis (this reduction in genetic diversity and changing allele frequency is sufficient to explain all diversity of life). But in order for this to be accepted as a scientific hypothesis, you can't just stop there. You need a model, you need to make predictions with that model and test those predictions. Otherwise, it is just a fantasy.

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 171 by Faith, posted 02-19-2014 6:33 AM Faith has not yet responded

  
snapdragon
Junior Member (Idle past 627 days)
Posts: 3
Joined: 01-20-2012


(3)
Message 174 of 233 (719905)
02-19-2014 9:56 AM


Intro to genetics...
As a terminal lurker, I wish this discussion had taken a different direction. It's an interesting discussion and everyone has brought up (mostly) good points, but for someone coming to the site for the first time and seeing "Introduction to Genetics", this ain't it. The actual frustration stems from, well, go back and reread the first post. This thread was created in response to Faith's questions about genetics and how we can determine ancestry, taxonomy, how morphology relates to genetics, etc. Anyone with an understanding of genetics and experience in education can see from how the questions are formed that what is really needed is exactly, an Introduction to Genetics. What DNA is, how it's replicated, what can go wrong in replication, that mutations aren't 'something breaking', that it is all just chemistry. Everything from replication to translation to a cute little six-toed kitten, it's all just chemistry.

Implicit in the original post's questions are many basic misunderstandings, and they are not and will not be addressed in the direction this thread has progressed. The original questions evoke a world where one creature has a genetic environment that is qualitatively different from that of another, that genes are quantized entities that are fractured by mutations...these are easily addressed once someone has a basic understanding of the structure of DNA. Questions like, where does "Junk DNA" come from, how do you determine relatedness of close family members, are all well-understood once you can grasp basic genetics. Now, once that evidence is presented, it doesn't mean that it won't be rejected out of hand, but at least statements like Taq's regarding mutations will have context, rather than being treated like non-sequiturs.

Again, this has turned out to be an interesting discussion, but I think Dr A's proposed series (Message 3) on introductory genetics will do a lot to raise the level of question and debate in the area of ancestry, mutations, and how things actually work. Carry on.


Replies to this message:
 Message 175 by herebedragons, posted 02-19-2014 10:14 AM snapdragon has not yet responded
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herebedragons
Member
Posts: 1328
From: Michigan
Joined: 11-22-2009
Member Rating: 5.9


Message 175 of 233 (719909)
02-19-2014 10:14 AM
Reply to: Message 174 by snapdragon
02-19-2014 9:56 AM


Re: Intro to genetics...
Welcome snapdragon ...

Actually, that is something I am planning to put together and hopefully I will have something up in a couple of days. I will be starting it in a new thread (since you are right, this one is going in a different direction) and I will keep your suggestions for topics in mind as go.

Implicit in the original post's questions are many basic misunderstandings, and they are not and will not be addressed in the direction this thread has progressed.

Agreed!

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


This message is a reply to:
 Message 174 by snapdragon, posted 02-19-2014 9:56 AM snapdragon has not yet responded

Replies to this message:
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Taq
Member
Posts: 6644
Joined: 03-06-2009
Member Rating: 4.1


Message 176 of 233 (719921)
02-19-2014 10:56 AM
Reply to: Message 169 by Faith
02-19-2014 1:10 AM


Re: Paradigm clash
Shown me? Where?

I will repeat my last post.

Among the 40 million mutations that separate humans and chimps are beneficial mutations that are responsible for the beneficial adaptations seen in both species. They are right there.


This message is a reply to:
 Message 169 by Faith, posted 02-19-2014 1:10 AM Faith has not yet responded

  
Taq
Member
Posts: 6644
Joined: 03-06-2009
Member Rating: 4.1


(1)
Message 177 of 233 (719924)
02-19-2014 11:04 AM
Reply to: Message 171 by Faith
02-19-2014 6:33 AM


Re: Factual versus interpretive tendentious terminology
Well I don't kid myself that anybody is going to accept my view of things to the point that there would be any need to rewrite anything. That would only happen if this creationist view were recognized as true. How soon you think that's going to come about?

The sooner you start pointing to facts instead of beliefs, the sooner your ideas have a chance of being accepted.

Im trying to make the point that the overall trend will always be to decreased genetic variability,

The problem is that a population that is increasing in number will also be increasing in genetic variability due to the accumulation of mutations in each generation. The chances of a neutral mutation reaching fixation is 1/n where n is the number of individuals in the population. The larger the population the lower the chances are that a neutral mutation will reach fixation meaning that a larger population will have a large number of neutral mutations that have not reached fixation.

The only time we see a drastic reduction in genetic variation within a population is if the population size is drastically reduced.

My point was that you CAN'T have an increase in genetic variability from a population split,

The accumulation of mutations after the population split does increase genetic variability over time. That is what happens in the real world.


This message is a reply to:
 Message 171 by Faith, posted 02-19-2014 6:33 AM Faith has responded

Replies to this message:
 Message 179 by Faith, posted 02-19-2014 2:34 PM Taq has responded

  
Taq
Member
Posts: 6644
Joined: 03-06-2009
Member Rating: 4.1


Message 178 of 233 (719930)
02-19-2014 11:22 AM
Reply to: Message 174 by snapdragon
02-19-2014 9:56 AM


Re: Intro to genetics...
As a terminal lurker, I wish this discussion had taken a different direction. It's an interesting discussion and everyone has brought up (mostly) good points, but for someone coming to the site for the first time and seeing "Introduction to Genetics", this ain't it. The actual frustration stems from, well, go back and reread the first post.

It is a rather large field to cover in a thread. It is much easier to answer specific questions, and we can't answer those questions until they are asked.

Feel free to pose some questions that may fill in the gaps in this thread.


This message is a reply to:
 Message 174 by snapdragon, posted 02-19-2014 9:56 AM snapdragon has not yet responded

  
Faith
Member
Posts: 25331
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 179 of 233 (719988)
02-19-2014 2:34 PM
Reply to: Message 177 by Taq
02-19-2014 11:04 AM


Re: Factual versus interpretive tendentious terminology
The problem is that a population that is increasing in number will also be increasing in genetic variability due to the accumulation of mutations in each generation.

Not many of which occur in the germ cells, though, isn't that correct? Not to mention that as usual the idea that the mutations actually accomplish anything for the benefit of the organism is an article of faith rather than shown to be fact.

The chances of a neutral mutation reaching fixation is 1/n where n is the number of individuals in the population. The larger the population the lower the chances are that a neutral mutation will reach fixation meaning that a larger population will have a large number of neutral mutations that have not reached fixation.

The only time we see a drastic reduction in genetic variation within a population is if the population size is drastically reduced.

Can you explain what the benefit is of "a large number of neutral mutations that have not reached fixation" ?

I do realize from this, however, that the tests I've proposed that involve examining the DNA for variability from population to population would be skewed by the counting of mutations that don't do anything toward the development of the phenotypes that define the subspecies. Is there any way to avoid this? Is it possible to focus only on the genes that clearly underlie the new phenotypes? (What is needed is a test to SHOW that mutations don't do what you all think they do. What tests have you done in this direction? That might show that mutations really ARE just mistakes and overall don't benefit the organism at all?)

(I'm thinking of observable traits, clear visible changes from the former population, although I know there would also be changes that wouldn't be observable.)

My point was that you CAN'T have an increase in genetic variability from a population split,

The accumulation of mutations after the population split does increase genetic variability over time. That is what happens in the real world.

But this is a completely artificial idea if the mutations don't actually DO anything to further the development of the character of the subspecies, and what interests me most about this now is if there is any way to differentiate between the mutations and alleles that are determining the new traits. I mean, can you tell for sure what IS a recent mutation, or is this the usual case of just assuming everything is as you assume it to be, such as that all those 40 million mutations are really alleles? That would certainly throw a wrench into the tests I have in mind.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 177 by Taq, posted 02-19-2014 11:04 AM Taq has responded

Replies to this message:
 Message 181 by Taq, posted 02-19-2014 2:55 PM Faith has responded

    
Faith
Member
Posts: 25331
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 180 of 233 (719990)
02-19-2014 2:43 PM


QUESTION ABOUT PSEUDOGENES
I agree with the person who said this thread isn't really "an introduction to genetics," it was originally for answering questions, mostly about the genome, and I think it got mistitled. But Dr. A said he had plans to do a genuine introductory course in genetics at some point.

=================
Anyway, I have a question about pseudogenes or "junk DNA" again. I understand these occur here and there throughout the genome. I'd like to know

1) if there's anything about them that meets the eye, just in their sequences or how they appear as you are sequencing the genome, to tell you they are not normal genes? Or do you have to do some kind of testing to see if they actually make proteins to find out that they aren't true genes?

2) what it is that has led geneticists to determine that some of them have a "regulatory function," and what that function actually is and how you tell? And how many of them can be described this way?

I think I have another question but I can't remember it right now.


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