the phylogeographic challenge to creationism

Well, I'll tell you what happened to Mendelian genetics - the model of dominance/recession is largely inapplicable to the majority of genetic interactions. A high school biology education will give you the impression that all or even most genes have only two alleles, where one is dominant and the other recessive, but they only do this because it's the simplest genetic model they can teach.The majority of genes are expressed either via incomplete dominance or codominance. The simple dominance that you're familiar with is more appropriate as a teaching tool, as a simple genetic model, than as a guide to the majority of genetic interactions.Of course, dominance itself only applies to diploid organisms. Asexual organisms have no dominance scheme because they have only one copy of each allele. The Mendelian model doesn't explain why a given gene has a dominant allele and a recessive one in the first place. You assert, I presume, that those alternate alleles were built in during the Creation week, or whatever; but the scientific observation is that mutation is responsible for these alternate alleles, and this explanation only contradicts Mendelian genetics in your mind. Certainly it doesn't in reality. Again you're using the word "phenotype" incorrectly. Phenotypic diversity is always indicative of genetic diversity. The word you're looking for is "species"; you're conflating isolated populations with individual morphological variation.

Yes I understand how Mendelian genetics work, and about alleles in the population and that should have been clear from many things I've said. you do not have to explain that. The difference is that now it is believed that there is no built-in coherent genetic picture that is segregated by hereditary transmission, it's all just tossed together by mutations and THAT's what's now considered to be segregated by hereditary transmission.I'm not sure it makes much difference when we are talking about the chipmunks in the OP. However you think the genetic picture was established, it WAS established, and when a portion of the population migrated what I'm saying happened happened. New phenotypes emerge as a result of the reproductive isolation and there is a corresponding reduction in genetic diversity in that new "species"/variety/breed.Please read what Mick wrote in Message 29 as he didn't find it hard to agree with how I described this process. In fact he continues to explain it all to jar in terms that agree with me in subsequent posts. You may have a problem with my layman's language but he didn't. The concepts are clear enough I think, and I'm not reaching beyond the little I understand either.It has not been proved that mutation does all this, that there is no built-in genetic complement. It has not been proved how much mutation is beneficial and how much disease, it has not been proved that the rate of beneficial mutation could possibly explain the segregation by hereditary transmission of genes, into many geographically separated coherent subspecies of anything over a relatively short period of time.This message has been edited by Faith, 11-28-2005 02:23 PM

I don't understand where you think anyone here has proposed that. Let me see if I can lay it out for you how it works under a Mendelian model where mutation occurs.Sexual organisms still inherit half of their chromosomes from one parent and half from another. They still inherit two copies of each gene, one from each parent (with the exception of certain genes on the Y chromosome). Sexual reproduction still results in recombination of these different alleles, and some of them are expressed acccording to a scheme of simple dominance, some according to a scheme of imperfect dominance, and some according to a scheme of codominance. Sexual recombination alone accounts for a fair bit of individual physical (or phenotypic) variation.But...Individuals also inherit genetic sequences from their parents that their parents did not themselves inherit; these new sequences are unique additions to the population's gene pool. Mutation is the source of these new alleles. Allow me to reiterate that this is proven scientific fact.Mutations aren't "tossing anything together." They're a source of new alleles in the population, and a source of variation among individuals. They're the reason that you look like the people in your family, but you don't look like the people in mine. No, they don't. New phenotypes emerge as a result of new geneotypes, which themselves result from sexual recombination and random mutation. New species result from reproductive isolation, and that does generally result in a loss of genetic diversity in the ancestor population, when the speciation is allopatric. Mutation is the built-in genetic component. It's built into our genetics that mutations will occur.

Just make an effort. Stop nitpicking. If you know what I mean then incorporate your correction in your answer. Making a huge production out of it is simply derailing the conversation. I'm no scientist and you know that, but I'm not stupid. Make an effort. The phenotype is the expressed traits of the creature as opposed to the genotype. In new "species" that are created by reproductive isolation as described in the OP, you have a NEW phenotype that characterizes the new variety/breed/"species", but you have reduced DIVERSITY of phenotypes just as you have reduced genetic diversity. In one scenario, in the parent population the new type was potential but recessive. That phenotype may never have occurred at all. It could only be expressed when the dominant genes were eliminated by reproductive isolation. So this is a NEW phenotype in the new population, that characterizes it, that makes it a "new species," but in order for it to occur genes that suppressed it in the ancestral population had to be eliminated. That reduces the overall NUMBER of genetic possibilities in the new population which reduces the genetic DIVERSITY in the new population adn also reduces the phonotypic diversity even though it has produced a new phenotype that characterizes the new species.If that isn't expressed exactly right, please reword it.The process of speciation DOES correspond to a reduction in genetic diversity and Mick had no problem recognizing this.

How about you make a fucking effort? You're not going to be able to understand my posts if you don't understand my terms; and if you insist that "reproductive isolation leads to phenotypic diversity" then you don't understand the terms you're employing.We're not going to play a game where I speak one language, and you speak your own. That's not how this works. You need to make the effort to employ your terms correctly. Otherwise what you're saying is just gibberish. Nobody knows what the fuck you mean, because you insist on speaking gibberish. Use the terms correctly, or don't use them. You don't get to simply substitute your own ideosyncratic definitions and then complain when we refuse to play along.It's time for you to grow up about this. Start using the terms correctly, or don't use them at all. Oh? "Stupid" is exactly how I would describe someone who, after being shown error, refuses to correct their behavior. Grow up about it, already. No, you don't. And this gets back to how you refuse to abandon the decades-discredited concept of species essentiallism. Species are not characterized as species because of physical characters; it's reproductive isolation that defines species. You can have two seperate species that are physically identical, with the exception of a genetic incompatibility that prevents interfertile hybridization. Over time, they develop morphological distinction, because of the interruption of gene flow between them; but that distinction is not an immediate result of reproductive isolation. Absolutely impossible, according to the Hardy-Weinburg model. If you have a situation of simple dominance, and the presence of recessive genes, you'll always have individuals who are homozygous recessive.Always. The original population will always have included these individuals, for as long as the recessive gene has been present. And where did the gene come from, originally? Mutation. And neither do I. I've been telling you this, now, for most of this thread. Is it just that you aren't paying attention, or what?This message has been edited by crashfrog, 11-28-2005 02:52 PM

There are too many people on this thread. The only ones I want to deal with are Mick, Modulous and maybe Mammuthus but I haven't read through his posts yet.This message has been edited by Faith, 11-28-2005 03:50 PM

You don't have to deal with people at all.You do have to deal with the issues or look like you can't.Sometimes one issue is given by more than one person. Just deal with it. If some of the individuals don't realize you have already dealt with an issue because you answered it for someone else that is their problem for not reading all the thread. (however, it might be nice to link to where you did when they query you on it).

Deal with whoever you want. What do I care? Just, employ the terms as they have been properly defined. Respond to corrections by correcting your behavior and usage.Don't shift the blame for your ignorance onto us.

That is asking too much.

Hi Faith, The problem with all of that is that it is an argument that leads nowhere. The whole argument "they are still Tamias" is just a red herring. It's a way of avoiding the question.Let's say we take Tamias amoenus (everybody must be bored of this stripy fellow by now) and Oryctolagus cuniculus (the rabbit). Let's see how far "they are still" can take us.Presumably you would accept that they are "different". One's a chipmunk and one's a rabbit, after all.Starting from the chipmunk we could say:1. Comparing Tamias amoenus in the north and Tamias amoenus in the south: They are still "yellow-pine chipmunk"2. Comparing Tamias amoenus and Tamias straitus: They are still chipmunk. Picture of striatus below. 3. Comparing Tamias amoenus and the genus Funisciurus: They are still "sciurinae". Picture of Funisciurus below. 4. Comparing Funisciurus and the genus Glaucomys: They are still "sciuridae". Picture of Glaucomys volans below. 5. Comparing Glaucomys with the genus Dipodomys: They are still "sciurognathi". Picture of Dipodomys spectabilis below. 6. Comparing Dipodomys to the genus Octodon: They are still "rodents". Picture of Octodon degus below. 7. Comparing Octodon to the genus Oryctolagus: They are still "glires". Picture of oryctolagus below. 8. Comparing Oryctolagus cuniculus with the genus Sylvilagus: They are still "rabbits". Picture of Sylvilagus floridanus below. 9. Comparing Sylvilagus with Lepus (the hare): They are still "leporidae". Picture of Lepus capensis below: 10. Comparing Lepus with the genus Ochotona: They are still "lagomorpha". Picture of Ochotona princeps below. 11. Comparing Ochotona princeps with Tamias amoenus: They are still "glires"........ Picture of Tamias amoenus below. So the "They are still..." argument allows us to travel between species, genera, subfamilies, families, orders, and superorders without ever accepting that "macroevolution" has taken place.It's a useless argument, it leads nowhere.Mickin edit: to clarify:Tamias amoenus and Tamias striatus are different species, but the same genus.
Tamias and Funisciurus are different genera, but the same subfamily.
Funisciurus and Glaucomys are different subfamilies, but the same family.
Glaucomys and Dipodomys are different families, but the same suborder.
Dipodomys and Octodon are different suborders, but the same order.
Octodon and Oryctolagus are different orders, but the same superorder.
Oryctolagus and Sylvilagus are different genera, but the same family.
Sylvilagus and Lepus are different families, but the same order.
Lepus and Ochotona are different suborders, but the same order.
Ochotona and Tamias are different orders, but the same superorder.One of these pairs of species MUST represent macroevolution even in the eyes of a creationist. Unless they are all "the same kind", in which case the question goes back to the opening post: where does the genetic structure between these pairs come from if it does not come from through microevolutionary processes?This message has been edited by mick, 11-28-2005 09:21 PMThis message has been edited by mick, 11-28-2005 09:24 PMThis message has been edited by mick, 11-28-2005 09:25 PM

Hi Mick,
I'm glad you returned. I wonder how far this can go. WHY should any of them represent macroevolution? Doesn't descent have to be proved for that purpose?The differing names themselves suggest a difference beyond the mere surface impression of similarity too, I would say. (You could probably breed a dog or cat to look amazingly like a rabbit but it would still behave like a dog or cat rather than a rabbit. Still wag its tail, bark at strangers, bare its teeth when threatened, slobber on its owner, need to be walked, sniff the ground and other dogs, mark its territory doggie style, fetch, in the wild run in packs; or catwise meow/roar, sharpen its claws on the furniture or tree trunks, use a litter box, mark its territory cat style, sit on a window sill for hours on end, like to hang out in high places, lay its ears back when displeased, stalk its prey, play with birds and mice before killing them. And yes I know that temperament and behavior are also breedable, but I suspect these behaviors would be just about impossible to erase. If you could breed all the typical behaviors out of a dog or cat and breed in the habits of a rabbit or chipmunk, THAT might impress me macroevolution-wise).If I knew enough about chipmunk behavior I would have used that example to argue that it will never act like a rabbit.This message has been edited by Faith, 11-28-2005 10:51 PMThis message has been edited by Faith, 11-28-2005 10:53 PM

Is this necessary? If you feel that way, why not ask her what she means, or allow the other posters that do want to respond to her in a civil manner do so without you spoiling the thread?Furthermore, I would like to weigh in here and say although I haven't read the whoel thread, Faith has a point in mentioning her interest in responding to several evo posters. She wants to respond to several evo posters, and if crash or someone has to resort to cussing her out to make his point, it is wrong to insist somehow she put up with that sort of verbal abuse. Regardless of whether she is right or wrong, such verbal abuse is unwarranted and wrong.From a cursory review, there appears to be some real discussion or potential for it. My suggestion is to allow that discussion to take place among parties interested in doing so in a civil manner.

Are you saying that massive morpholigical change would still not be macroevolution, and the deciding factor is behaviour?What if the brain changed as part of the morphological change?

Hi Faith,
I realize you are getting a bit piled on in this thread. Focus on the posts you wish to deal with and let the others slide as randman suggested. Also, most of us are not trying to belittle you. There are some basic concepts that you have misunderstood and aside from mick's OP, I am trying to help clear them up.

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Yes I understand how Mendelian genetics work, and about alleles in the population and that should have been clear from many things I've said. you do not have to explain that. The difference is that now it is believed that there is no built-in coherent genetic picture that is segregated by hereditary transmission, it's all just tossed together by mutations and THAT's what's now considered to be segregated by hereditary transmission.

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The problem is you do not understand how Mendelian genetics works. Even Mendel recognized that new variants can spontaneously arise. His problem was that he could only look at variants that had a dramatic effect on the phenotype (in his case color or morphology) of the plants he studied. Currently, we can look at the changes in the DNA sequences that are responsible for the phenotypic changes. These changes in the DNA sequence occur at random by mutation. All transmissible variation in a population is due to mutation. An allele is a mutant version of a different allele. What we call wild type is usually the most frequent version of an allele like red eyes in Drosophila. It is an arbitrary designation...if you had started with a purple eye population of Drosophila, then wild type would be purple.

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The difference is that now it is believed that there is no built-in coherent genetic picture that is segregated by hereditary transmission

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It was never believed that there was build in coherent genetics. Even prior to molecular biology, new mutants appeared from pure stocks via mutations. It was recognized early on that radiation and chemicals that damage DNA can lead to a higher rate of the appearance of new variants because it changes the underlying DNA sequence. Genetics is the study of mutation and how it is passed on.
As to coherent genetics..no such thing...if you have kids, they represent novel mutants as they will carry novel alleles generated by mutation that do not occur in either your genome or that of your husbands.

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New phenotypes emerge as a result of the reproductive isolation and there is a corresponding reduction in genetic diversity in that new "species"/variety/breed.

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This is also incorrect. The phenotype did not emerge due to isolation. A rare phenotype may become common do to isolation but it may have been present in the original population. Otherwise, it would work like this, you have one population that gets split into two by geography or whatever. Gene flow between them is no longer possible. By random mutation in every generation, they will diverge from one another even without selection because every individual born carries new mutations. Since the populations cannot breed with each other, they will diverge and diverge to the point that even if they were to come into contact again, they would not be able to breed. This is observed in the lab and in the wild. There are other ways for speciation to occur but in this case, there would only be a reduction in genetic diversity if one of the two original populations was very small...and over time, as a small population grows, it gains diversity by random mutation...this has also been demonstrated in the lab and in the wild.

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Please read what Mick wrote in Message 29 as he didn't find it hard to agree with how I described this process. In fact he continues to explain it all to jar in terms that agree with me in subsequent posts. You may have a problem with my layman's language but he didn't. The concepts are clear enough I think, and I'm not reaching beyond the little I understand either.

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Mick is asking you to address a somewhat different issue. Not the origin of variation among populations, species, and higher taxonomic levels but rather what is the difference in the process. Why do you think and can you support that the processes that separate a rabbit from a chipmunk are different from those that separate two different chipmunks? I am explaining (at the nitty gritty level) that the processes and how they are measured are identical whether you are comparing to breeds of dog from a rabbit and an elephant.

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It has not been proved that mutation does all this, that there is no built-in genetic complement.

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In fact it has repeatedly been "proved". It is a known biochemical fact from the known replication error frequencies of all the polymerases known (and sold on the market for that matter). It has been observed and cataloged in bacteria, yeast, flies, humans, etc. etc. So you statement is just plain wrong. What has never been demonstrated is a build in genetic complement in any species.

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It has not been proved how much mutation is beneficial and how much disease,

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It really depends. It has certainly been shown in bacteria and in flies with mutation load studies. In humans there are specific cases which are quite well characterized such as malaria resistance and balancing selection for the sickle cell trait. But I may be misunderstanding you statement.

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it has not been proved that the rate of beneficial mutation could possibly explain the segregation by hereditary transmission of genes, into many geographically separated coherent subspecies of anything over a relatively short period of time.

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Actually, the beneficial mutation rate is relatively unimportant in this case. The markers analyzed are neutral markers that do not influence phenotype. And this has been successfully done in thousands of species.The study of beneficial mutations is more difficult and not as advanced. Mostly because beneficial is a relative statement. What is beneficial in one environment can be a catastrophe in another so that selection goes back and forth over time. In the lab it is much easier to show the effects of beneficial mutations than in the wild.Your post is fine as are your questions. But I would avoid making absolute statements of what scientists know or don't know until you are a bit more familiar with the field. One cannot pretend that thousands of studies just don't exist.Let me know if any of the explanations I posted are unclear.

Mick understood what I meant by "suppressed" in terms of dominance and recession and didn't treat it as an invalid point. "Low frequency" is fine. Point is that when they are selected and reproductively isolated they generate a new race or breed or what evolutionists now call a species, and the very process of selection is the reduction of genetic diversity available to them.If the scientists insist on being scientifically exact I will give up or take the discussion to the religion side of the board. Snowing nonscientists under with scientific technicalities, burying the forest in the trees, and berating them for their failure to use scientific concepts as scientists do IS belittling them.Many times it has been recognized, even on this board, and Mick did so early in the thread, that the [AbE: majority of the] processes of speciation do in fact reduce genetic diversity. That's what natural selection does, and bottleneck, and so on, MOST OF the processes that isolate portions of a gene pool (I have carefully avoided saying ALL), these being the processes that I keep finding labeled Evolutionary Processes. THEREFORE, the very same processes that supposedly lead to evolution do it by reducing genetic diversity. Some sites actually address this as a problem, especially in domestic breeding. So why I can't get this one simple fact established here is a puzzle to say the least. The ideas that this process IS the process that generates all genetic material, or that it necessarily produces anything evolutionarily useful at all, still seem conjectural to me. I have been trying to be careful to avoid saying ALL and to acknowledge that there are some exceptions, saying only that the majority of the processes that select and isolate populations, that are labeled Evolutionary Processes, do have the effect of reducing genetic diversity. Who said it did? The point is the TREND. ANY reduction at all is a reduction. I have carefully acknowledged that. Nevertheless the majority of them do have this effect -- natural selection, founder effect, bottleneck, migration etc. ONLY mutation and recombination (reintroducing populations to each other that are capable of interbreeding?) appear not to. And you say something else is going on with the cichlids but I can't follow it so until you translate it I don't know what the situation is there. What I can grasp of it -- it appears to be a discussion about separate clearly related populations that do not interbreed -- doesn't suggest anything in favor of macroevolution or any different kind of mechanism than we are discussing -- but since it is technically over my head you will have to break it down for me. I didn't state it in the caricatured way you are doing. It is one thing that does occur and Mick didn't have a problem recognizing it. See his discussion with jar earlier in the thread, that starts with jar's Message 31. I wasn't talking about individuals but about genetic potentials. Again Mick appeared to know what I was saying. 1/100 expression is as good as suppression as I was using the term. And in the new population that 1/100 is going to become characteristic of it, and in order for that to happen the 99 other variants in the parent population have been eliminated, and THAT means there is sharply reduced genetic diversity in the new population -- in that trait anyway -- and correct me if I'm wrong, but when one trait is clearly selected by population isolation, surely many others are too.Please try to reduce technicalities in your answer to this.This message has been edited by Faith, 11-29-2005 02:39 PM