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Author Topic:   A test for claimed knowledge of how macroevolution occurs
caffeine
Member (Idle past 292 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 166 of 785 (854982)
06-14-2019 4:11 PM
Reply to: Message 133 by Percy
06-13-2019 5:21 PM


I guess I don't see traditional breeding and mutation breeding as the same thing. The examples you mentioned of mutations in dogs and cattle have come up in previous discussions, and I wasn't forgetting them when I said that mutations play almost no role in breeding. Your sense that mutations have been responsible for more breeding results than we give credit for seems a quite a stretch to me, though I would of course concede in the face of evidence. But that populations of domestic breeds revert so quickly to wild forms once out in the wild (see, for example, When domesticated animals return to the wild) argues strongly, at least to me, against mutations playing any meaningful role in breeding.

Dogs have loads of mutations presumed to have arisen since domestication. The only one I can think of off the top of my head (other than the stumpy legs one) is the duplication of the amylase-producing gene. But dogs are a special case since they've been domesticated so much longer than anything else (and feral dogs don't revert to wild-type - dingoes are not wolves); so I'm not going to waste time looking up more examples in dogs.

MC1R is a very famous gene, since it's effect on coloration makes its mutations obvious, and since variation in MC1R plays a role in some of the most immediately obvious variation amongst humans. For the same reasons of obvious phenotypic effect, MC1R has been extensively studied in other animals. Wild boar, for example, are monotypic for MC1R - all wild animals have the same allele. Domestic pigs, however, have at least four different MC1R alleles, which contribute to the huge variation in colour of domestic breeds. Now, it is of course possible that the ancestral wild population contained all these alleles, which have coincidentally been lost by drift in the reduced wild population. It seems much more likely to me, though, that these are all post-domestication mutations which have spread once pigs were removed from the selective constraints of camouflage. This sort of thing has presumably created the canvas from which breeders have selected in many domesticated species.

A lot of the most obvious examples are about colour, but there are many other well-known examples. Check these chickens:

The chap on the top right is monotypic for the wild-type allele. The other three show varied combinations of the rose-comb and pea-comb mutations. These mutations are not known in wild jungle fowl - they are unique to domestic chickens. And it's extraordinarily unlikely that these mutations exist in the wild. Breeders have tried repeatedly to establish pure rose-comb breeds (for aesthetic reasons) but keep failing; for the fairly simple reason that roosters homozygous for the rose-comb allele have sperm that can't swim straight.

Texel sheep (a breed originating from an island off the north coast of the Netherlands) are renowned for their high meat content. The genetic basis of this has recently been pinpointed to a mutation in the GDF8 gene, which produces myostatin. They're not as impressive looking as Belgian blue cattle, but you can see they're kind of built

Again, this is a mutation presumed to have arisen since domestication. Above are only a few examples, but I found dozens in a very quick Google search, and am pretty confident I can keep listing them for a while.

To be clear, I don't think I'm proposing anything novel. I think it's pretty well established that domestic breeds incorporate a range of mutations either seized upon by breeders; or which have simply been allowed to spread by drift in the absence of the selective pressures present in the wild. Reversion to wild type often involves selection against these alleles that are beneficial or neutral in a stable, but detrimental in the wild. Or, you get something like pigeons, who even in their feral state maintain many of the phenotypes developed under domestication - just not the ones that are detrimental to survival without a human carer.

Edited by caffeine, : No reason given.


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AZPaul3
Member
Posts: 6732
From: Phoenix
Joined: 11-06-2006
Member Rating: 2.9


Message 167 of 785 (854984)
06-14-2019 4:13 PM
Reply to: Message 165 by Faith
06-14-2019 3:35 PM


Re: Tracking the route of macroevolution
Where I used to think a single trait such as eye color was probably governed by many genes, it seems now that it's governed by different regions of a single gene??????

Just to muddy your waters: One gene, one protein went out years ago. We know now that the control sequences inform the transcription RNAs where to begin and end transcription. They can direct transcription to any part of the gene and even cause segments to be transcribed multiple times, all to make one specific protein. A single gene can thus be transcribed into multiple different proteins.

Such a process is called alternative splicing and the resultant proteins are called isoforms.

And if that's not complex enough the control mechanisms can even produce specific proteins from transcribing different regions of separate genes. Cross gene alternative splicing.

Eye color is dependent on a number of items like melanin and other proteins in the leaves of the iris. Some isoforms some not. Some cross gene isoforms.

Chemistry is fun.


Eschew obfuscation. Habituate elucidation.

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caffeine
Member (Idle past 292 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(2)
Message 168 of 785 (854985)
06-14-2019 4:28 PM
Reply to: Message 148 by AZPaul3
06-13-2019 10:10 PM


Re: Tracking the route of macroevolution
Oh, she knows. She gets it. But the religion is still in the way.

I think you're very wrong. She doesn't get it. Sure, her opinion is coloured by her religious opinions; but if we approach every disagreement with Faith as if she understands all the words we're using in the same way as we do but pretending not to, we're never going to get anywhere. I do not get the impression she is intentionally misunderstanding. Rather, in constructing a model that conforms with her religious beliefs, she has come to conceive of certain biological concepts in different ways than we do.

I don't think Faith is pretending to misunderstand us. I think instead that she's internalised definitions for concepts we think she understands that are different to the definitions we mean. I don't see the value in accusing her of lying. Better, like Taq is trying to do, to explain what we actually mean. And let's try to understand what Faith is trying to say - otherwise, what's the point of talking to each other?


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caffeine
Member (Idle past 292 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(1)
Message 169 of 785 (854986)
06-14-2019 4:37 PM
Reply to: Message 107 by Faith
06-13-2019 2:53 PM


Re: Tracking the route of macroevolution
What I want is a hypothetical mutation or series of mutations that do more than just change the protein for a trait built into the genome of a given species.

But why would you ask for such a thing, given that we're talking about the differences between chimps and humans.

Chimps and humans have exactly the same organs. All of them. We have exactly the same bones. All of them. They're all in the same place. And everything is made out of the same stuff.

Not exactly the same, of course. As we discussed in a previous thread, there are slight differences between human and chimp keratins. But these differences are small and simple, and quite probably non-functional. I would be willing to bet that if you replaced the gene that produces human fingernail keratin with the gene that produces chimpanzee fingernail keratin, you would not notice - the fingernails would like the same.

Few, if any, of the 40 million odd mutations separating us from chimps would have a large and noticeable effect. But 40 million is a huge number. All 40 million together have a very noticeable effect - it's the difference between a human and a chimp.

But there are literally no major structural changes necessary to move between a chimp and a human. What differences do we have from chimps that are not simply changes in the colour, size and shape of existing structures?


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AZPaul3
Member
Posts: 6732
From: Phoenix
Joined: 11-06-2006
Member Rating: 2.9


Message 170 of 785 (854990)
06-14-2019 5:52 PM
Reply to: Message 168 by caffeine
06-14-2019 4:28 PM


Re: Tracking the route of macroevolution
I’m not so sure. I think she can see the processes we present. She just cannot accept them.

She is resistant, because of religion, to any system, realistic or not, that challenges the catechism. That’s why she opposes evolution.

But that resistance also extends to learning what evolution is and is not. As a consequence the lady has accumulated a whole bunch of wrong ideas about how the chemistry actually works.

We have an opportunity to maybe, just maybe, change a wee bit of that by showing that evolution does not work in her straw man way. That mutation is not the disaster she is led to believe. That genomes are not static. That minor change by minor change, micro step by micro step, the phenotype of a far future lineage of dog will vary significantly from any dog today because the future dog gene pool will be considerably different from the dog gene pool of today.

She doesn’t want to entertain such reasonable notions since they don’t fit the straw man she thinks she has defeated.

Maybe we can’t make her into an evolutionist. But, we may be able to educate her away from some the more preposterous processes her straw man entails.

Maybe not.

Edited by AZPaul3, : No reason given.


Eschew obfuscation. Habituate elucidation.

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Dr Adequate
Member (Idle past 319 days)
Posts: 16112
Joined: 07-20-2006


Message 171 of 785 (855007)
06-15-2019 2:09 AM
Reply to: Message 170 by AZPaul3
06-14-2019 5:52 PM


Re: Tracking the route of macroevolution
This has been tried. Even if she can understand what's been said to her she won't remember it and then a few months later it'll all be to do again.

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Faith 
Suspended Member (Idle past 712 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 172 of 785 (855009)
06-15-2019 2:43 AM
Reply to: Message 168 by caffeine
06-14-2019 4:28 PM


Re: Tracking the route of macroevolution
Thank you. I'm sure there are things I'm misunderstanding but I also have the impression that the definitions of things change every time there's a new episode of this kind of discussion. I get the idea for instance that there are many genes for a particular trait, and the next time the subject comes up, no, it's that a single gene can make a protein or proteins that make many different traits, and so on and so forth. I don't even know if it really matters since when I try to get into a new version of the discussion I end up with a similar answer each time anyway.

The main thing seems to be that you all see mutations where I see normal built in variation and this has never been satisfactorily sorted out. Even if you can show me some mutations in the mix the overall process by which the variation occurs still doesn't need the mutations as I see it, the normal alleles are quite sufficient for creating all the variations that make new phenotypes.

I've argued this over and over and over again and I think it still holds but you are always throwing new things at me and haven't REALLY addressed my arguments. My main argument is that to get new phenotypes all that has to happen is reproductive isolation of a portion of a species population. This can happen as genetic drift within the population or it can happen as geographic isolation away from the main population. The new isolated population merely has to reproduce for some number of generations to create a completely new set of phenotypes, even a new "species." This is because of the new set of GENE FREQUENCIES that the founders of the new population carry with them. I acknowledge that there may be complicating factors going on as well but I do believe this is the basic formula for creating a new "species" from a larger population, though it's really the same species, just now changed because of the new gene frequencies. This is why I point a lot to "ring species" where phenotypic changes occur from population to population around some kind of geographic obstacle. You all believe this is due to mutations. I don't. I think the only thing necessary is the isolation of a small number of individuals from the previous species/population. All it takes, ALL it takes is a new set of gene frequencies brought about by this isolation of a portion of the previous population breeding together for whatever number of generations it takes to blend the new alleles into a new phenotypic presentation.

I've given the examples that came up years ago many times too. The Pod Mrcaru lizards that developed from five pairs that were released onto an isolated island. Thirty years later scientists found that the descendants of those five pairs had developed very large heads and jaws and were eating tougher stuff than the parent population. There were also changes in the gut as I recall. In only thirty years. Muations again were assumed and again I say, no, that is not necessary, the genes built into the creature are all that's necessary. When you isolate a small number of individuals you get new gene frequencies that bring out new traits. THAT IS ALL YOU NEED. YOU DO NOT NEED MUTATIONS. And this demonstrates too that evolution, which is of course microevolution in this case, does not take much time at all. It was thirty years before they were seen again but it's possible the whole population had changed some time before that.

Then there were the Jutland cattle, or was it sheep, whatever. This herd of whatever it was had spontaneously split into four smaller herds that somehow got reproductively isolated, by preference perhaps as in genetic drift, or some geographic isolation, I'm not sure. It's been a long time. But the point of the story that was posted here was that striking changes developed in each of the four different groups in a very short period of time. Microevolution again, no need for mutations, completely new phenotypic presentation in short period of time.

I also bring up the wildebeests, the African gnus that form a huge herd, millions I think. They all look alike, but there is a smaller population some distance away that has a different look to it. The big population is called I think the black wildebeests, the smaller population is called the blue wildebeests because there is a bluish tone to their hide. The blue wildebeests all look alike too. Nobody knows in this case but my guess is that the blue group started with a small number of individuals that wandered off and got isolated from the main herd. They would have had a set of gene frequencies that differed from the main herd's and all that had to happen to bring about their different appearance was being reproductively isolated among themselves for some number of generations until their new traits blended and they became a new "species" as it were. Smaller than the main herd, bluish where the main herd was brown or black, different form of antlers too I think. Enough differences anyway to mark them off as a separate "species."

Dogs and domesticated cattle are also examples I've used, and I've even suggested a laboratory experiment with mice. I think all that ever happens is that I get ignored or insulted, told I just don't understand evolution etc., or evos come along and insist it's all due to mutations and that's the end of the discussion. Maybe they can even show a mutation or two, but that's not enough to defeat this general argument.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


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Faith 
Suspended Member (Idle past 712 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 173 of 785 (855010)
06-15-2019 2:52 AM
Reply to: Message 170 by AZPaul3
06-14-2019 5:52 PM


Re: Tracking the route of macroevolution
She is resistant, because of religion, to any system, realistic or not, that challenges the catechism. That’s why she opposes evolution.

No, the reason is that I have a coherent other theory or explanation for the changes you all impute to mutations. As I just argued for the umpteenth time above. I suppose Dr. A or someone else thinks that's been answered, but it hasn't. Really it can't be because it has to be true.

Edited by Faith, : No reason given.


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Faith 
Suspended Member (Idle past 712 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 174 of 785 (855011)
06-15-2019 3:12 AM
Reply to: Message 170 by AZPaul3
06-14-2019 5:52 PM


Re: Tracking the route of macroevolution
We have an opportunity to maybe, just maybe, change a wee bit of that by showing that evolution does not work in her straw man way. That mutation is not the disaster she is led to believe.

That genomes are not static.

Despite all your proliferating hundreds of alleles you haven't shown that a species genome ever changes to the extent of producing something outside its built-in variations. This might be difficult because you don't believe in such variations, you ascribe it all to mutations. This may be why this discussion never goes anywhere. It isn't a matter of evidence, but a matter of commitment to our own model.

That minor change by minor change, micro step by micro step, the phenotype of a far future lineage of dog will vary significantly from any dog today because the future dog gene pool will be considerably different from the dog gene pool of today.

You haven't shown this and you can't show it. All dog breeds have reduced genetic diversity, in some cases depleted to the point of fixed loci for all the major characteristics, which used to be how a purebred was defined, and there is simply no further variation possible beyond that genetic condition. So you aren't going to get your future dog gene pool from any established breed.

You'll say, Oh but mutations... Well, once you've got such reduced genetic diversity mutations become destructive rather than helpful. Consider the cheetah with its severely depleted genetic diversity. They hope for a beneficial mutation to improve its health but it hasn't happened and unfortunately a deleterious mutation could wipe them out.

If you want to start with a mutt rather than a breed you'll have more genetic diversity to work with but you'll have to prevent it from becoming a breed or "new species" , probably by continually mating it with other mutts to keep up the genetic diversity and increase it. Actually all or most of the breeds would revert to mutts anyway **** on their own so you'll have a lot to work with. The problem with that is that you never will get a new species of dog, because that does require reduced genetic diversity which brings variation/evolution to a halt.

Yeah I know: Oh but mutations....

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


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PaulK
Member
Posts: 17169
Joined: 01-10-2003
Member Rating: 2.5


(1)
Message 175 of 785 (855012)
06-15-2019 3:31 AM
Reply to: Message 172 by Faith
06-15-2019 2:43 AM


Re: Tracking the route of macroevolution
quote:

Thank you. I'm sure there are things I'm misunderstanding but I also have the impression that the definitions of things change every time there's a new episode of this kind of discussion.

I think you will find that that is almost all your misunderstanding.

quote:

I get the idea for instance that there are many genes for a particular trait, and the next time the subject comes up, no, it's that a single gene can make a protein or proteins that make many different traits, and so on and so forth

And in this case it certainly is your misunderstanding. Aside from the fact that there is no change of definition at all, this is just the reality being more complicated than you assumed. A gene can contribute to many traits and many genes can contribute to a trait - there is no contradiction there. And when you remember what real genes actually do it shouldn’t even be a surprise.

quote:

The main thing seems to be that you all see mutations where I see normal built in variation and this has never been satisfactorily sorted out

As we have seen you can see “normal built in variation” even when we are talking about mutations - where there is no doubt at all. That shows where the main problem is.

quote:

I've argued this over and over and over again and I think it still holds but you are always throwing new things at me and haven't REALLY addressed my arguments. My main argument is that to get new phenotypes all that has to happen is reproductive isolation of a portion of a species population

Now that may be true, but what has to be explained is not just “new phenotypes” but new species. And variations that go beyond the limits observed in breeding. Even in breeding mutations occur and are used in shaping new phenotypes - so regardless of what is “needed” mutations are going to play a part.

And let us not forget that you insisted that bottlenecks would produce new phenotypes - even claiming the elephant seal and the cheetah as examples. Yet you never pointed to even one phenotypic change in either species.

quote:

This is why I point a lot to "ring species" where phenotypic changes occur from population to population around some kind of geographic obstacle.

But you have never shown that “ring species” support your ideas. They are entirely consistent with standard evolutionary theory which you reject.

quote:

You all believe this is due to mutations. I don't. I think the only thing necessary is the isolation of a small number of individuals from the previous species/population.

I suggest that all breeding can do is to create a motley collection of phenotypes while additional mutations are needed to explain new species - at least in the general case.

quote:

Then there were the Jutland cattle, or was it sheep, whatever. This herd of whatever it was had spontaneously split into four smaller herds that somehow got reproductively isolated, by preference perhaps as in genetic drift, or some geographic isolation, I'm not sure. It's been a long time. But the point of the story that was posted here was that striking changes developed in each of the four different groups in a very short period of time. Microevolution again, no need for mutations, completely new phenotypic presentation in short period of time.

And yet none of them is a new species.

quote:

I also bring up the wildebeests, the African gnus that form a huge herd, millions I think. They all look alike, but there is a smaller population some distance away that has a different look to it. The big population is called I think the black wildebeests, the smaller population is called the blue wildebeests because there is a bluish tone to their hide.

And how do you know that mutations weren’t involved in the separation of the two species ? You keep giving us what you claim are examples but you never show that they support your claims.

quote:

Dogs and domesticated cattle are also examples I've used, and I've even suggested a laboratory experiment with mice. I think all that ever happens is that I get ignored or insulted, told I just don't understand evolution etc., or evos come along and insist it's all due to mutations and that's the end of the discussion.

I think you have got it the wrong way round. You are the one who usually ignores or insults people and accuses them of not understanding - and you insist that your ideas are right and that’s the end of discussion. Consider this whole long post - you don’t produce any real evidence at all. You don’t get to win by just insisting you are right - even if we didn’t have evidence.


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Faith 
Suspended Member (Idle past 712 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 176 of 785 (855013)
06-15-2019 3:33 AM
Reply to: Message 175 by PaulK
06-15-2019 3:31 AM


Re: Tracking the route of macroevolution
I am not going to go through this same argument with you again for the umpteenth time. Sorry. Time to let caffeine or AZPaul argue it. If they want to rephrase what you are saying that's up to them. I'd prefer something new myself.

Edited by Faith, : No reason given.


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Tangle
Member
Posts: 8547
From: UK
Joined: 10-07-2011
Member Rating: 2.4


(1)
Message 177 of 785 (855014)
06-15-2019 3:34 AM
Reply to: Message 174 by Faith
06-15-2019 3:12 AM


Re: Tracking the route of macroevolution
Faith writes:

Despite all your proliferating hundreds of alleles you haven't shown that a species genome ever changes to the extent of producing something outside its built-in variations.

For the umpteenth time - it took 15 years of work but the mutation that caused the white peppered moth to turn black in the early 19th century has been found. This is an example of a beneficial mutation that ensured its survival. The exact thing that you say can't happen.

quote:
After a long time we eventually managed to get down to a single one [DNA differences between black and white moths] which then had to be the causal mutation. To our surprise, it also turned out to be a rather unusual type of mutation."
The carbonaria mutation was in fact a "jumping" piece of DNA, called a transposon, which had inserted itself into a gene called cortex.
These odd sequences more often have a damaging effect when they disrupt an existing gene. But for one embryonic moth in the early 19th Century, when these extra 9,000 bases landed in its cortex gene, they were in fact the secret to success.

http://www.bbc.co.uk/news/science-environment-36424768


Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. I am Mancunian. I am Brum. I am London.I am Finland. Soy Barcelona

"Life, don't talk to me about life" - Marvin the Paranoid Android

"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.


This message is a reply to:
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Faith 
Suspended Member (Idle past 712 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 178 of 785 (855015)
06-15-2019 3:36 AM
Reply to: Message 177 by Tangle
06-15-2019 3:34 AM


Re: Tracking the route of macroevolution
The pocket mice are a similar example. So what. That is not what this argument is about.

This message is a reply to:
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PaulK
Member
Posts: 17169
Joined: 01-10-2003
Member Rating: 2.5


(1)
Message 179 of 785 (855016)
06-15-2019 3:38 AM
Reply to: Message 176 by Faith
06-15-2019 3:33 AM


Re: Tracking the route of macroevolution
quote:

I am not going to go through this same argument with you again for the umpteenth time. Sorry. Time to let caffeine or AZPaul argue it. If they want to rephrase what you are saying that's up to them. I'd prefer something new myself.

In other words you have had genuine answers - and know it - and you are the one who simply insists on their opinions “end of discussion”.

Thanks for admitting to that, even if it was only implicitly


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Tangle
Member
Posts: 8547
From: UK
Joined: 10-07-2011
Member Rating: 2.4


(1)
Message 180 of 785 (855017)
06-15-2019 3:42 AM
Reply to: Message 178 by Faith
06-15-2019 3:36 AM


Re: Tracking the route of macroevolution
Faith writes:

So what. That is not what this argument is about.

It's EXACTLY what the argument is about. You say that beneficial changes to the genome can't be made by mutation. This is proven to be wrong.


Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. I am Mancunian. I am Brum. I am London.I am Finland. Soy Barcelona

"Life, don't talk to me about life" - Marvin the Paranoid Android

"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.


This message is a reply to:
 Message 178 by Faith, posted 06-15-2019 3:36 AM Faith has replied

Replies to this message:
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