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Author Topic:   A New Run at the End of Evolution by Genetic Processes Argument
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(2)
Message 112 of 259 (770938)
10-16-2015 8:30 AM
Reply to: Message 96 by Faith
10-14-2015 9:55 PM


Some "intelligent" questions
There must be some INTELLIGENT QUESTIONS that could be asked about my claims instead of this you aren't a scientist and you have no right to challenge our sanctified theory attitude you all have.
OK. I have a few questions based on your "genetic depletion" premise.
Do changes or differences in a gene count as diversity if they are in a non-coding region such as introns or intergenic spacers and have no discernible effect on phenotype? And could those polymorphisms allow identity with a particular group or population to be adequately made? In other words, what criteria identifies a sub-species with the larger species group?
Would you predict that a family such as Orchidaceae or Asteraceae, with more than 20,000 species each, would have low diversity or high diversity? Should breeding programs with orchids continue attempting to create new varieties, or have they run out of diversity yet? If they have not run out of diversity, then why have they not, with more than 20,000 species. Or what about Drosophilidea which has over 3,000 species, some of which are used extensively in genetic studies and are known for the high amount of diversity they exhibit? Your idea seems to predict Drosophila melanogaster should be depleted of genetic diversity, but its not. Drosphilidea, Ochidaceae and Asteraceae all have had way more branching events than Felidea, of which cheetahs are a member; yet cheetahs suffer genetic depletion because of those branching events and the others mentioned do not. Why?
Since total genetic diversity, which it seems to mean the sum total of all the alleles at all loci in a population, is for all practical purposes impossible to measure at this time (I don't think you realize what a daunting task measuring something like that would be) could you recommend a surrogate measure? Are there genetic markers that would provide a good estimate of genetic diversity?
What method do you use to determine how closely related populations are? If a population splits and the daughter population becomes a new sub-species and then that daughter population splits again and the split becomes a grand-daughter population, the grand-daughter population will be more closely related to the daughter population than it is to the parent population, right? So, what criteria do you use to determine which is the daughter population and which is the grand-daughter population and can you give an example of this methodology being applied to real populations?
Further expanding the above idea, if population splits occurred very rapidly after the flood bottleneck we should now have great, great, great, great, great grand-daughter populations living as extant sub-species. If fact, the grand-daughter populations would have split off to make aunt and great aunt populations as well.
Would you be able determine ancestry based on genetic diversity data? Here's what I mean... you suggest that some population in the past had very high genetic diversity and as sub-populations split off from that population, they lost diversity. So, it would seem that groups with high genetic diversity are more ancestral than populations with low diversity, which would be the derived form. In other words, could we take the dog group and arrange it based on genetic diversity, come up with some sort of branching tree-like structure and have a good idea how the dog group developed? Based solely on genetic diversity. Can you give an example of a study that used that or a similar methodology?
Finally, in cladistics we refer to all species that share a common ancestor as a monophyletic group. Your scenario would have the same situation; all species or sub-species that descended from the original ark pair would form a monophyletic group or clade. What criteria would you use to determine which monophyletic group a sub-species belongs to? For example, does a fox and its kin belong to the wolf/dog clade or does it belong to a different clade (maybe the fox clade) and what criteria do you use to determine that?
I am not sure you will consider any of these questions to be "intelligent," but these are the kinds of things I find troubling about your scenario. These are issues that I don't think your "genetic depletion model" can address, but the standard genetic model does address quite well. How could I use this model in my own population study? Why should I adopt this model when the model I already have appears to work so well, and I don't see any practical way to apply this model (nor does it even seem plausible)?
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 96 by Faith, posted 10-14-2015 9:55 PM Faith has replied

Replies to this message:
 Message 123 by Faith, posted 10-16-2015 2:48 PM herebedragons has replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(4)
Message 113 of 259 (770942)
10-16-2015 9:18 AM
Reply to: Message 88 by NoNukes
10-14-2015 6:19 PM


Re: What is the definition for speciation in play here.
The only thing that keeps male dogs way from female dogs are size differences
This alone would be enough to reproductively isolate populations in the wild - Great Danes would not be able to mate with Chihuahuas for instance and could be considered biologically distinct species. Some people consider dogs to be an example of a ring species, separated not by geographical location, but by morphology.
What is the definition for speciation in play here.
To be fair, "species" is a very contentious subject. Every taxonomist has his/her own criteria for what should be classified as a separate species. There are of course general guidelines and some very useful definitions, but they can't be universally applied in all situations and a lot of subjectivity comes into play when assigning taxonomic categories.
Ultimately, classification of species, sub-species or whatever, is a human construct used to convey particular information about a particular population. Referring to Great Danes and Chihuahuas as sub-species of the wolf conveys particular information about those population's habits, purpose, relationships, etc. just as referring to lions and tigers as separate species (although they can make viable hybrids) conveys particular information about those population's habits, habitats, locale etc.
Faith's attempt to rename recognized species as sub-species is really just an attempt to distance her idea from the concept of macroevolution. However, it is completely unnecessary and confusing. Taxonomy is used for the convenience of human discussion, the organisms don't care whether we call them species or sub-species. Even were all species created as is 6,000 years ago, we would still be able to classify them in this hierarchical system of species, genus, family etc. based on shared characteristics. So what hierarchical system is used is really irrelevant.
What we would not be able to do (or would not expect to be able to do) if every species were created as is, is to attach any significance to ancestry based on those classification systems. However, we CAN significantly attach information about ancestry to our classification system and just calling something a sub-species does not change that.
* I am pretty sure you know all this, but you asked
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 88 by NoNukes, posted 10-14-2015 6:19 PM NoNukes has replied

Replies to this message:
 Message 116 by RAZD, posted 10-16-2015 10:46 AM herebedragons has not replied
 Message 121 by NoNukes, posted 10-16-2015 1:25 PM herebedragons has not replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 140 of 259 (771013)
10-16-2015 10:26 PM
Reply to: Message 123 by Faith
10-16-2015 2:48 PM


Re: Some "intelligent" questions
Nitpick: It's not a "premise," it's the conclusion.
No, it's not really a conclusion. You have made some observations and are trying to explain those observations. Maybe you have presented an hypothesis, but hypotheses are "If..., then..." statements, so what you have presented is not an hypothesis. So, its a premise; it is your starting position which you assume to be true.
I'm talking about observable recognizable changes in the phenotypic presentation of a species, so if it doesn't affect those changes then no it doesn't count.
So then to be clear, we are not talking about genetic diversity, but phenotypic diversity... perhaps allelic diversity; but not genetic diversity.
In the species/family as a whole sounds like high diversity. But I'm not interested in what happens to the species/family as a whole.
When animals came off the ark, they would have been the start of a new family of animals (let's assume that family is roughly equivalent to "kind"). So, what happens to the family as a whole IS important to your argument. A family of organisms is made up of individual species and if the individual species are genetically depleted, the whole family is genetically depleted.
This is just another example of not wanting to deal with ALL the evidence.
Plants may be genetically different enough from the animals I have in mind to need a different explanation, I don't know, but if animals haven't run out of genetic diversity after beaucoup population splits into beaucoup new subspecies, it's because they started out with tons of heterozygous genes and no junk DNA.
This is assuming the conclusion and is why your whole point is a premise rather than an hypothesis. You have no evidence that the original population started out with "tons of heterozygous genes and no junk DNA," you assume it is true because you assume your initial premise is true.
You know plant genetics and I don't and fruit flies too I guess. Sounds like they have lots more genetic possibilities than animals.
Flies are animals. But either way, you keep wanting to avoid discussing anything that contradicts your premise.
Lots of stuff like polyploidy or that sort of thing?
Polyploidy would be mutation, no?
Unless the principles involved are entirely different, however, I would assume that plants too would eventually run out of genetic diversity.
You would assume... but do they? Is there evidence that plants are running out of diversity?
Again you are asking questions that I don't think can be answered
Cannot be answered by your premise, which is precisely my point.
I really have no idea what the problem is. Just as a general statement, if one model is true and another false you'd be better off with the true one even if you've adapted to the false one, right?
Yes, of course we would be better off with the "true" model. The problem is, how do we know what the "true" model is? We test it. We use it to make predictions. We use it to solve problems and answer questions about the world. We really have no way to know for certain that any model is the "true" model, but we can determine the BEST model considering the information we currently have.
My questions were to assess how well your model could work to answer questions scientists ask.
But all I'm interested in is what a sequence of new subspecies that require reduced genetic diversity does to the ToE.
That's the whole problem, Faith, you are not looking for the best model to explain the evidence you are simply looking to discredit the ToE.
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 123 by Faith, posted 10-16-2015 2:48 PM Faith has replied

Replies to this message:
 Message 141 by Coyote, posted 10-16-2015 11:10 PM herebedragons has not replied
 Message 142 by Faith, posted 10-17-2015 12:05 AM herebedragons has replied
 Message 149 by Faith, posted 10-17-2015 3:49 PM herebedragons has not replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(3)
Message 162 of 259 (771049)
10-17-2015 11:42 PM
Reply to: Message 142 by Faith
10-17-2015 12:05 AM


Re: Some "intelligent" questions
You seem to be in a mood to find things to accuse me of.
I am not trying to accuse you of anything. I assume that you are trying to present your views in good faith and I don't suspect any "skulduggery." But your position is faulty; it doesn't match up with the reality that we work with every day. What you are doing is focusing on a few general observations and extrapolating those observations to the whole ToE despite there being observations that invalidate your conclusions. If you want us to concede that evolution caused a reduction in genetic diversity in cheetahs, elephant seals and domestic breeding populations, I think we already have. I said it a long time ago that yes, it's true, but trivially true. PaulK has said it, and I believe Dr. A, RAZD and Percy have agreed as well; it's true, but trivially true. It is not the whole story.
My examples and questions were meant to challenge the idea that evolution REQUIRES a reduction in genetic diversity and that as organisms evolve they will eventually run out of genetic diversity. Groups of organisms that have undergone multiple speciation (or sub-speciation, whatever) events have NOT run out of diversity. That challenges the idea that evolution REQUIRES a loss in diversity.
it reminds me that the loss of genetic diversity through processes of evolution is definitely a conclusion I came to from my own encounters with evolutionist concepts.
No. You may have reached a conclusion based on your study but when you apply it to a broader scope, like addressing the ToE, it becomes a premise. After you have formed your premise then you need to form the hypothesis such as: If evolution reduces genetic diversity then we should observe groups that have undergone multiple speciation events to have significantly reduced genetic diversity. Now before you can draw a conclusion about your premise, you need to run tests and/or examine the data based on your hypothesis.
What data do you have on, for example, dogs? Do you have any genetic diversity information on dogs at all? Can you demonstrate that any breeds have less genetic diversity than the breeds they were derived from?
If no, then you cannot make a conclusion as to whether your premise is true or not.
from Message 146
Apparently I missed the "challenge." I don't get it. The whole thing hits me as a series of incomprehensible accusations of this or that fallacy or error, based on some preoccupations of HBD's own that have nothing to do with what I've been arguing.
Incomprehensible?? You have actually been studying this issue longer than I have. How is anything I said or asked incomprehensible?
My questions DO have everything to do with what you are arguing. You claim that your ideas completely discredit the ToE, and yet you only want to focus on a few unique cases where the species have low genetic variability. Certainly not enough to convince me to change the direction of my research. Nor do I see that your premise has any bearing on the ToE in any significant way. Certainly doesn't discredit it; doesn't really even challenge it.
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 142 by Faith, posted 10-17-2015 12:05 AM Faith has replied

Replies to this message:
 Message 169 by Faith, posted 10-19-2015 5:32 PM herebedragons has replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(4)
Message 178 of 259 (771092)
10-19-2015 11:42 PM
Reply to: Message 169 by Faith
10-19-2015 5:32 PM


Re: Some "intelligent" questions
but now I’m sure you just don’t understand the argument I’m making, which is in fact par for the course here so I should have known it before.
Of course we don't understand it, because if we did we would certainly abandon the ToE in favor of your much more well thought out approach.
You are talking about plants. As I said plant genetics must be appreciably different from the animal situations I tend to focus on, and I’m not sure exactly how or how it might make a difference to my argument, and so far you have done nothing to clarify this,
Plant genetics works just like animal genetics and fungal genetics and bacterial genetics. That is why we use plants like Arabidopsis and fruit flies like Drosophila melanogaster and yeast like Saccharomyces cerevisiae and even round worms like Caenorhabditis elegans as genetic models which have helped to work out cellular processes and gene function in humans. Yes, plants and insects and yeast have different survival and reproductive strategies, but the underlying genetics works the same way; as do evolutionary processes. We don't need a different theory for every kingdom.
As I believe I said I have to assume that the overall genetic situation is similar enough that if I’m right then plants too will lose genetic diversity with each new population split,
Data please. Support these kinds of statements with data.
Meanwhile please leave my personal experiences to me.
Personal experiences aren't data. You can keep them to yourself if you wish.
I believe I discovered a rule about how the processes of evolution work, the selective or subtractive processes. If that is the case it should apply across the board wherever those processes are operating.
That does not appear to be the case. I pointed out some examples where it doesn't appear to apply. So should it apply "across the board," or not?
In the case of dog breeding and other breeding programs I most certainly can. There is absolutely no doubt that breeding from selection of traits requires loss of genetic diversity. This is what makes domestic breeding such a good example for what must happen in all similar situations.
Then where is your data?
Well, it just so happens that I poked around a little and found this paper. It's not plants, it's not insects, it is exactly the subject you are talking about. Here are the basics:
They studied 100 microsatellite markers in 28 dog breeds and determined heterozygosity, percentage of loci in H-W equilibrium and % of total number of alleles in each breed.
Here is figure 2 where they have plotted the above data by year each breed was registered.
quote:
It was also of interest to determine if the number of alleles per breed differed relative to the totality of alleles observed in all breeds, and to what extent this was influenced by population size and time since registry recognition. The total number of alleles observed for all breeds and loci was 1,780. Within each breed, a range of 399 to 805 alleles per breed was found, with an overall average of 605 alleles (Table 1). The number of alleles per breed mirrored the level of heterozygosity (Figures 1 and 2). As a function of population size, the breeds with smaller populations had about 6% fewer alleles than the breeds with larger populations. When plotted as a function of time since recognition by a registry, the numbers of alleles observed per breed was lower for the earlier recognized breeds by about 7%.
Note that the earlier recognized breeds had 7% FEWER alleles on average than the more recent breeds. Also notice that the trend line for heterozygosity INCREASES as the breeds get younger. Both trends are in opposition to your premise.
Of course, Figure 2 uses time since registration, not time since the breed split off from a parent breed. So let's look at this phylogeny of dog breeds.
And let's compare that to table 1 from the above paper: (I deleted some breeds from the table because they weren't listed on the tree)(HBa is average breed heterozygosity; SDHa is standard deviation of HBa)
AKC group BreedHBa SDHa
Herding Pembroke Welsh corgi.630 .017
Border collie .669 .018
Australian shepherd.696.012
Hound Borzoi.605.021
Greyhound .648.017
NonsportingBulldog.581 .020
Chow chow .666 .017
American Eskimo dog .686 .014
SportingLabrador retriever .641.016
Golden retriever .657.016
Brittany spaniel .666.014
TerrierBull terrier .387 .021
Miniature bull terrier.474 .019
Jack Russell terrier.758.012
Toy DogsPug.566.017
Yorkshire terrier .684 .018
Papillon.698 .013
Pomeranian .705 .014
WorkingBoxer.474 .023
Doberman pinscher .527 .017
Akita .642 .018
So lets look at a couple of examples and compare their heterozygosity:
Labrador retrievers earliest then Golden retrievers: Prediction: Labrador > Golden
Data: Golden - .657; Labrador - .641 Conclusion: Falsified
Pomeranian earliest then Papillon then Pug. Prediction: Pomeranian > Papillon > Pug
Data: Pomeranian - .705; Papillon - .698; Pug - .566 Conclusion: Supports
Borzoi earliest then Greyhound. Prediction: Borzoi > Greyhound
Data: Borzoi - .605; Greyhound - .648 Conclusion: Falsified
Pembroke corgi earliest then Border collie then Australian sheep dog. Prediction: Pembroke > Border collie > Ausi sheep
Data: Pembroke - .630; collie - .669; Ausi - .696 Conclusion: Falsified
Awww Snap. It doesn't look good for the theory of genetic depletion.
because as you say it is impossible to measure genetic diversity in most cases and I would expect these examples to make the general case about genetic diversity.
No. I said the way you are expecting genetic diversity to be measured is all but impossible at this time. Researchers do genetic diversity studies all the time. They just don't measure every allele at every loci in every individual.
Your straw man version of my argument certainly wouldn’t challenge it.
So you keep saying that no one understands your argument, but is it not more likely that you don't understand the rebuttals?
HBD
Edited by herebedragons, : No reason given.
Edited by herebedragons, : clarification
Edited by herebedragons, : clarified relationship between Labradors and Goldens

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 169 by Faith, posted 10-19-2015 5:32 PM Faith has replied

Replies to this message:
 Message 179 by Faith, posted 10-20-2015 1:48 AM herebedragons has replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(3)
Message 189 of 259 (771112)
10-20-2015 9:03 AM
Reply to: Message 179 by Faith
10-20-2015 1:48 AM


Re: Some "intelligent" questions
Since you think thousands of plant species disproves my argument, you DON'T understand it, as I said, since all that would mean is great genetic diversity in plants.
But that's assuming the conclusion, Faith. I pointed this out previously.
And what about the polyploidy? Is that a common phenomenon in plants?
Yes, it is common in plants but does occur in some animals as well Polyploid animals. The problem is that polyploidy is a mutation caused by non-disjunction during meiosis. It's a well known, observed phenomenon.
Please HBD, don't give me bright white charts which are hard to read. Please just explain the point you think they make. Explain the numbers in your own words please.
My apologies, I did forget about your eye troubles. However, I did explain the chart in my own words and included the author's caption to the chart.
The chart shows a trend of increasing heterozygosity and % of the total number of alleles as the breeds become more recent. If the "rule" was that breeds LOSE genetic variability the trend line should be decreasing. Newer breeds should, on average, have less heterozygosity than older breeds.
As for the claim that recent breeds have a higher number of alleles,
That is not a "claim," it is what the data shows.
that could reflect the change in breeding practices from the severe selection methods they used to practice to the more careful attention to keeping the genetic diversity high enough to protect the animals' health.
Even so, the diversity is not just remaining high, but increasing. You claim breeding REDUCES genetic diversity.
I looked up Golden Retriever since on your chart it is said to have been bred from the Labrador,
I should have changed the Lab example like I did the others because "bred from" is not exactly the correct term I should have used. The Labrador was developed earlier and the Golden was developed later (in the same line of descent).
Did you even read the quote from Wikipedia?
quote:
Marjoribanks had purchased Nous in 1865 from an unregistered litter of otherwise black wavy-coated retriever pups.
If the chart got that wrong perhaps it got other things wrong too. If you breed different animals together you get a hybrid and the allele count should go up of course. Also the article suggests that the actual line of descent of many breeds is not known.
Breeding is clearly not a straightforward process and does not produce true tree-like branching. A true breeding phylogeny would be a network consisting of hybrids all over the place. This tree shows mitochondrial DNA inheritance I believe, would show maternal descent. The Wikipedia article does say that the Golden retriever was descended from the a retriever and then hybridized with another breed.
Besides, reading up a little on the history of the breeds in the retriever group (Newfoundland, Labrador, Golden, and Flat-coated) the chart seems fairly accurate to me. The interbreeding is definitely a lot more complicated that the tree shows, which as you say would introduce alleles into a breed and increase diversity.
But if that is how breeding works, you don't have a case anyway. Breeding isn't just simple population splits and subsequent reduction in diversity.
The study I linked shows that diversity of dog breeds has increased over time, not decreased as you say it should have. I don't know what else to say about it.
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 179 by Faith, posted 10-20-2015 1:48 AM Faith has replied

Replies to this message:
 Message 194 by Faith, posted 10-21-2015 6:06 PM herebedragons has replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 210 of 259 (771415)
10-25-2015 8:38 PM
Reply to: Message 194 by Faith
10-21-2015 6:06 PM


Re: Your "falsifications" are falsified
I will have to make this brief, hopefully I will be able to come back to this discussion later in the week.
But again only SELECTIVE breeding is what I’m talking about. Cross breeding ADDS ALLELES, it’s a completely different form of breeding. My whole focus is on what happens genetically due to SELECTION AND ISOLATION.
If that was the entirety of your argument, then this discussion is a total waste of bandwidth. We agreed long ago that that type of breeding DOES reduce genetic diversity; it removes alleles just as you say.
Here is the exchange from 2013 from my first encounter with you on this issue
HBD writes:
I did not say that artificial breeding does not reduce genetic variability. It does and in that she was largely correct.
Faith writes:
Hip hip hooray. I may have to copy that out, change the font to something formal like Olde English and put it in 72 point and hang it on my wall. Yikes, a tiny little concession. Means SO much.
But what she seemed to imply was that breeding is accomplished by eliminating genetic diversity alone.
Faith writes:
Yes, that is indeed my argument. You do not get new breeds, new phenotypes, either in the wild or under domestication, or keep an established breed pure, without reducing the genetic diversity, or once the breed is established, by keeping the genetic understructure limited to ONLY what expresses the characteristics of that breed.
But that selective breeding reduces genetic diversity is NOT the whole of your argument is it? You have said that selective breeding is the ONLY way to create new breeds, species, varieties, or whatever. You have said that selective breeding is a DIRECT comparison to natural selection and therefore, evolution is wrong.
However, it doesn't appear that you can find even one example of selective breeding from the sources I referenced that shows reduced genetic diversity. You instead find cross breeding that introduces new alleles into a population and the new breeds are developed from there. So new breeds are made by crossing and reinforced or fixed by selecting.
Well you should have recognized that when a dog was registered says nothing about it genetically, and that brings the study itself into question. To say anything about my argument you’d have to have dogs in a direct line of descent. That doesn’t seem to be the case with the dogs on this chart.
I did recognize that and even mentioned it in my post, which is why I supplied the phylogenetic diagram as well.
Why should more recently registered dogs have higher genetic diversity? The only reason I can think of is what I said earlier, that they may not have been as severely selectively bred as earlier breeds.
No, when breeds were developed and when they were registered does not correlate perfectly. But since breeds don't have a "made on" date attached to them and instead were developed over periods of time, registration seems to be a valid surrogate. Also, a breed can only be registered when they have a suitable sized breeding population, so when a breed is actually "developed" is kinda vague, instead registration is when they were officially recognized as a breed.
There are a couple out-of-place breeds on the chart I presented (the Akita and the American Eskimo are two) but, the list appears to be in a general sense ordered from oldest breeds to youngest breeds. But if you want to take a look at table 1 and reorder the list from oldest breed to youngest breed I could create a new chart with a new trend-line.
But keep in mind, we are looking for a TREND here. There is strong selection in breeding (much stronger than we would find in natural populations), so if your hypothesis is true, genetic diversity should be getting depleted in dog breeds over time. Overall, new breeds should have less diversity than older breeds. I know you say that it has nothing to do with you argument since it isn't exclusively "selective breeding," but if that's truly the case then I don't see how domestic breeding works as an example of your hypothesis since domestic breeding relies heavily on cross breeding - introducing new traits into an existing genetic background.
If we were to find a gene that provided resistance to a particular disease, we would not just try and select for that trait, we would try to cross that trait into a variety that has a desirable genetic background - such as high yielding, upright growth, whatever characteristics that particular crop requires. Selection is hardly the only tool in a breeders toolkit.
Genetically that means absolutely nothing and it’s hard to fathom why anyone would even do such a study or think you could find out anything about the genetics of the breeds from it.
Right, that is why I presented the phylogenetic study. I tracked down the original source of the phylogram and the source is listed below. Unfortunately it is behind a paywall. I was able to download it at work, but when I tried to post the link, I couldn't get access.
**Pollinger, John P., et al. "Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication." Nature 464.7290 (2010): 898-902.
It's a good study and does mean something genetically. It was published in Nature, a very highly respected journal, so I trust that it has been adequately peer-reviewed. A couple of quotes from the article:
quote:
we analysed more than 48,000 single nucleotide polymorphisms (SNPs) typed in a panel of 912 dogs from 85 breeds as well as an extensive sample of 225 grey wolves (the ancestor of the domestic dog) from 11 globally distributed populations
quote:
The radiation of modern dog breeds has been difficult to resolve because most have originated recently and lack deep, detailed histories. Consequently, the evolutionary process underlying the genesis of phenotypic/functional groupings is obscure. Specifically, many breeds have been documented as originating through crosses of genealogically or geographically distant stocks and thus, parallel evolution and genetic heterogeneity within phenotypic/functional breed groupings is expected. Nonetheless, we discern distinct genetic clusters within modern dogs that largely correspond to those based on phenotype or function, including spaniels, scent hounds, mastifflike breeds, small terriers, retrievers, herding dogs and sight hounds
quote:
Notably, toy and working dogs have a more varied relationship to genetic groupings, which is consistent with their known histories involving crosses between breeds from divergent genetic lineages. The heterogeneous composition of toy breeds may specifically indicate their frequent origin as a cross between a larger dog from a distinct breed grouping and a toy or dwarfed breed
quote:
Finally, within each breed, there is a remarkable concordance with known origin as all dogs are correctly assigned to the breed or population from which they were sampled, with one exception (bull terrier and miniature bull terrier).
While I don't expect that this study gives us an exact reconstruction of the history of dog breeds, it does shed some light on the genetics of dog breeds. We know that genes are inherited from the parents and so genetic studies like this are helpful to resolve genealogical histories. So this tree shows where a particular breed got its genes from (or at least the markers the authors studied).
So, the Labrador, the Golden retriever, Flat-coated retriever and Newfoundland all share a common ancestor. The Newfoundland was derived from this ancestral stock first. The St. John's water dog (now extinct) was developed from the Newfoundland. The Labrador, Golden and Flat-coated all began from bedding stock that had it's beginnings in the St. John's water dog. Thus this cladogram matches reasonably well with what is known about the history of the retriever group.
To prove anything about my argument they would have to be in a direct line of descent by selective breeding only.
That is an unrealistic expectation considering the complexity of breeding programs. Do you have any examples of breeds, varieties, species that are the direct result of the type of "selective only" breeding programs you are describing? If so, present them and we can try to see if we can find any diversity studies on those organisms.
If nothing else, this should demonstrate that evolution (even evolution by artificial selection) is not a straight forward process, but is messy and includes many diverse processes besides just selection.
I have already spent way more time here than I should have, so I need to wrap this up now.
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 194 by Faith, posted 10-21-2015 6:06 PM Faith has replied

Replies to this message:
 Message 211 by Faith, posted 10-28-2015 11:31 PM herebedragons has replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 215 of 259 (771788)
10-29-2015 11:07 PM
Reply to: Message 211 by Faith
10-28-2015 11:31 PM


Re: Your "falsifications" are falsified
Thanks for a good reply that should help to move things forward.
Your charts have made it clear that selection isn't the dominant method I thought it was, but you are also wrong to claim that a mixture of cross breeding and selection could show that reduced genetic diversity doesn't occur as I've been claiming. It CAN'T occur if you include additive processes and I do think I've been very clear about that.
This is a confusing point. What the charts showed was what DOES occur; "additive process" plus "selective processes" tended to INCREASE diversity. I am not trying to show that selection CANNOT reduce diversity, I already agreed that it can (although I have previously shown ways that selection can INCREASE diversity as well). But what we observe happening in both breeding populations and natural populations over time is a TENDENCY to increase genetic diversity - because there is always "additive processes" at work. The chart shows that the general trend in dog breeds has been an increase in genetic diversity (as measured by heterozygosity).
So the overall number was 1780 and the breeds varied between 400 and 800. THIS should be broken down and studied among other things, if it's possible from those charts to find any actual genetic lines of descent that could be pursued for the purpose. The number of alleles is what we need to be looking for, but only where you know the line of descent and it's all selective. Even with cross breeding the numbers in that study show an obvious reduction from the parent population, whatever it was in each case.
This is based on the assumption that the parent population (ancestral wolf) had all 1780 alleles, this is not necessarily the case. In fact, this study only looked at 100 markers so, in the original ark population of 2 individuals there could only be 400 alleles maximum at those markers (2 alleles per loci x 100 loci x 2 individuals). So... where did the additional 980 alleles come from??
There is no need to do that once I've presented the data from Wikipedia on each breed (in Message 194) showing the utter lack of genetic relatedness. If a Wikipedia article written presumably by people familiar with that particular breed doesn't have the exact genetic history, how can we be sure that phylogenetic chart has it all right?
The phylogenetic chart was built as an representation of the relationship between the genes, so it specifically addresses the genetic relationships. No, it's not certain that it is 100% accurate, but it does give significant insight into the genetic history of dog breeds. We have come a long way in developing statistical models that give us high confidence in the phylogenetic hypotheses we develop from studies like this.
That's where my idea of a laboratory experiment came in, where you take some kind of small animal, say maybe twenty individuals, and let them breed freely, then take out a number of individuals from the resultant population into another cage or area and let them also breed freely and keep doing that as long as you are getting new phenomes. When you aren't I would assume you've reached genetic depletion.
I don't get why you equate stability of a phenotype with depletion of genetic diversity... Hardy-Weinberg. Allele frequency will come to equilibrium rather quickly, although in a small population drift will may a significant role. However, drift won't make the entire population homozygous.
Yes, of course, which I've said half a billion times myself in one way or another, but nevertheless the point I'm making is ONLY about selection, and what I've been claiming is that that is the only direction of evolution that really IS evolution, that could conceivably lead from species to species. HOWEVER, it IS messy and I DO have to figure out how to say more clearly why the additive processes couldn't. I know they couldn't but that's not very convincing.
And the dog breeding example shows that evolution also works through "additive processes" as well (cross breeding to create new breeds). Natural evolutionary processes can also involve hybridization and stabilizing selection (that increases or maintains diversity). So we should understand how ALL processes work, not just one particular piece that seems to support your position.
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 211 by Faith, posted 10-28-2015 11:31 PM Faith has replied

Replies to this message:
 Message 218 by Faith, posted 10-30-2015 3:14 AM herebedragons has replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 216 of 259 (771789)
10-29-2015 11:20 PM
Reply to: Message 214 by Faith
10-29-2015 6:37 PM


Re: Moderator Clarification and Requests for Same
The illustrations of the four different modes show the separation of a portion of a population. All four of them. I NEVER mean only geographic isolation, I ALWAYS mean reproductive isolation.
Please explain how you can get reproductive isolation without geographic isolation.
I am pretty convinced that there are no true examples of sympatric speciation. Cases where species have diverged in the same geographical area are actually cases of "micro-alleopatric" speciation where populations are kept separated within the same habitat (niche partitioning is a good example).
We have talked about this before, the important issue is reduction in gene flow. Sympatric has the greatest POTENTIAL for gene flow but for some reason, gene flow does not occur at a high enough rate to offset the tendency of the two populations to diverge genetically.
What factors would significantly reduce gene flow?
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 214 by Faith, posted 10-29-2015 6:37 PM Faith has replied

Replies to this message:
 Message 217 by Faith, posted 10-30-2015 2:36 AM herebedragons has not replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 219 of 259 (771811)
10-30-2015 8:42 AM
Reply to: Message 218 by Faith
10-30-2015 3:14 AM


Re: Your "falsifications" are falsified
I will just take a minute to explain what genetic markers are and what they mean.
A genetic or molecular marker is a section of DNA at a known location on a chromosome that is associated with a particular gene or region. Primers are used to bind the end of the fragment so that polymerase can copy the strand. A forward and reverse primer are used which generates a fragment of a specific length based on the sequences between them. Ideally the primers are located in a highly conserved region (such as an exon) and the amplified region is a highly variable region (such as an intron). Below is an example of such a marker - the so called ITS1 marker.
The left and right facing arrows show the position and directionality of the primers. They are located in the 18S and 5.8S ribosomal subunits, which are highly conserved - meaning that almost all fungal ribosomal RNA genes will have this sequence (it will probably amplify other kingdoms as well, but I am not sure to what extent). The sequence that lies between those two conserved regions - identified as ITS-1 is highly variable, meaning it varies greatly among different species and even among isolates of the same species, because it is an intron (clipped out during ribosome assembly). It is used to identify isolates to species.
This is too confusing for me to figure out. For starters I didn't think they were talking about the supposed original wolf population. Beyond that I don't know if the dogs on the ark all looked like wolves or what they looked like. And I also don't know how you get back to the ark with any of this information anyway. Even the oldest breeds can't be traced anywhere near that far back.
I am only talking hypothetically here. I thought it was agreed that dogs were breed from wolves and there would have been a pair of wolf/dogs on the ark. It doesn't matter that we can trace any particular breed that far back, but the implication is that all dog breeds came from a single ancestral breeding pair. If that is the case, then the number of alleles in the original pair at these markers could not have been more than 400 total number of alleles - that would have been maximum heterozygosity. Remember, we don't care what they "looked like," we are looking at the pattern of genetic inheritance and the number of alleles present.
Perhaps you have a different idea of what dogs were on the ark? AIG "scientifically" determined that the level of "kind" for dogs is at the family Candiae
quote:
Canidae (Dog kind)
There are 13 genera and 35 species of canids (Wilson and Reeder 2005). There is considerable hybrid data, including a cross between a coyote and a red fox. This has led to the suggestion that fewer genera should be recognized because these animals are quite closely related (Van Gelder 1977). A number of creationist studies have been done, including a couple which examine diversity within the family (baraminology studies summarized in Lightner 2009; Pendragon 2011; previous baraminology studies summarized in Wood 2006). The strong cognitum and extensive hybrid data suggest the kind is likely at the level of the family.
Mammalian Ark Kinds
So it is not unreasonable for me to speculate that all dog breeds derived from a single "dog kind" pair on the ark since that is what creation scientists believe, and if that is true, total number of alleles has INCREASED 350% since then. Hmmm....
Another conundrum...
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 218 by Faith, posted 10-30-2015 3:14 AM Faith has replied

Replies to this message:
 Message 220 by Faith, posted 10-30-2015 12:07 PM herebedragons has replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 221 of 259 (771835)
10-30-2015 1:03 PM
Reply to: Message 220 by Faith
10-30-2015 12:07 PM


Re: Your "falsifications" are falsified
I don't know what a "primer" is but you go on as if I do.
dna primer
I have no idea why a strip of fungal DNA should give any information about anything other than fungi.
It is an EXAMPLE of a marker. The markers used in the study use the same principle, just target different regions of the genome. However, you may be surprised to know that you also have ribosomal RNA genes just like fungi. In fact, human 5.8S rRNA is 75% similar to a yeast 5.8S rRNA. So if the only information you have is a piece of 5.8S rRNA, you could correctly identify if that fragment was from a yeast, a human, a dog, a chimp, etc.
As for wolves, I thought the study was merely talking about the sum total of alleles in the registered dogs they studied, not the whole dog population.
What's the difference? Wouldn't you expect the entire population to have MORE total alleles? Your position is that the founding population had MORE alleles than the total number of alleles in all daughter populations - or at best, if no alleles have been lost they would have the same number of alleles. No new alleles can be created - according to you. There is 1780 alleles or MORE in the entire population.
In any case I have no idea what you mean about 400 alleles on the ark or how you get that from the DNA markers.
Each individual can only have a maximum of 2 alleles at each marker - you know this right? There are 100 markers that they sequenced and counted the number of different alleles. An individual that is heterozygous at every marker they studied would have a sum total of 200 alleles at those markers (100 loci markers x 2 alleles per loci). Two individuals that did not share any alleles in common would have a sum total of 400 alleles (200 alleles/individual x 2 individuals).
This is a completely incomprehensible post to me.
Come on Faith. You have been studying this topic for over 10 years and have no concept of the BASICS??? I really thought you were trying. Or... are you simply feigning ignorance to avoid having to deal with the implications?
**** The original pair of "dog kind" animals on the ark could NOT have had 1780 alleles at these 100 loci. That would be 17.8 alleles per loci. Where did all the extra alleles come from??? Mutations perhaps???
HBD
Edited by herebedragons, : No reason given.

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 220 by Faith, posted 10-30-2015 12:07 PM Faith has replied

Replies to this message:
 Message 222 by Faith, posted 10-30-2015 1:21 PM herebedragons has not replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 228 of 259 (771871)
10-31-2015 12:49 PM
Reply to: Message 224 by Admin
10-31-2015 9:27 AM


Re: Moderator Suggestion
You're not the only one having trouble following these long posts that cover a lot of territory
I would appreciate it if it was pointed out when something in my post(s) is unclear or hard to follow, even if it has to come from Admin. I tend to try to abbreviate my explanations for time's sake and may fail to make some details clear; and yes, sometimes I try to cover a lot of territory. "I don't understand this concept or this line of argument" is completely appropriate, but "your post is completely incomprehensible" is just not - I am not a incomprehensible, babbling buffoon. It just seems like an avoidance strategy to me.
So please, call me out if my points are not as clear as they should be.
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 224 by Admin, posted 10-31-2015 9:27 AM Admin has seen this message but not replied

Replies to this message:
 Message 229 by Faith, posted 10-31-2015 12:54 PM herebedragons has not replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 230 of 259 (771873)
10-31-2015 1:01 PM
Reply to: Message 227 by Faith
10-31-2015 11:28 AM


Re: Reliable Mutations
DNA processes themselves are wonderfully precise, unbelievably complex and yet orchestrated to an amazing perfection. How DNA replicates itself, which we've all seen illustrated in various animations, is truly awesome in the way that word should be used. The basic system itself ought to be regarded as evidence for a Creator. The organization, the precision that is required for the reproduction of life is breathtaking, yet you all believe it just came together out of mindless physical ingredients?
I agree, and the more I learn about how natural systems work, the more I am convinced of a Creator. Personally, I don't believe that it all came together out of "mindless physical ingredients."
However, personal incredulity is not an effective system to use to determine how the world actually works.
Why don't you distinguish between mutations in body cells and those in sex cells? Those in body cells are completely irrelevant to evolution because they don't get passed on.
I take it you mean this as a rhetorical question, because I am skeptical that you would really be open to the explanation.
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 227 by Faith, posted 10-31-2015 11:28 AM Faith has replied

Replies to this message:
 Message 231 by Faith, posted 10-31-2015 1:09 PM herebedragons has replied
 Message 236 by Faith, posted 10-31-2015 2:23 PM herebedragons has replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 232 of 259 (771878)
10-31-2015 1:20 PM
Reply to: Message 225 by Faith
10-31-2015 9:52 AM


Re: Moderator Suggestion
If the question is simply where did the alleles come from above and beyond the two for each locus that had to have been in the individuals on the ark, I've said there had to have been a form of mutation to account for them. A very reliable form of mutation I might add, that actually formed alleles instead of mistakes, unfunctioning alleles or diseases, a mutation rather different from that we know today.
Yes, I guess I did miss where you postulated "a very reliable form of mutation." Would this be of the type where the polymerases know what mutations are needed and deliberately make nucleotide substitutions that the organism needs to evolve? Or is it divine intervention?
Seriously, instead of speculating what must be true because your premise is true, let's talk about how things ACTUALLY work.
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 225 by Faith, posted 10-31-2015 9:52 AM Faith has replied

Replies to this message:
 Message 234 by Faith, posted 10-31-2015 1:41 PM herebedragons has not replied

  
herebedragons
Member (Idle past 858 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 233 of 259 (771883)
10-31-2015 1:34 PM
Reply to: Message 231 by Faith
10-31-2015 1:09 PM


Re: Reliable Mutations
If you could keep that in mind, I'd be happy to hear an explanation.
Will do. Just let me know what you don't understand... it can't be everything.
what I mind is accusations that I'm not "open" to this that or the other for underhanded reasons.
I apologize, but it often feels that way, and I am not the only one who gets that impression. But I will try to be more patient.
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 231 by Faith, posted 10-31-2015 1:09 PM Faith has replied

Replies to this message:
 Message 235 by Faith, posted 10-31-2015 1:43 PM herebedragons has replied

  
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