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Author Topic:   the phylogeographic challenge to creationism
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 136 of 298 (264598)
11-30-2005 9:56 PM
Reply to: Message 134 by mark24
11-30-2005 7:34 PM


Re: Trying to get reoriented so I won't give up
My answer is the same, you have no reason to claim NS reducing diversity is a block to evolution when mutation introduces it all the time.
If a mutation introduces a deleterious or neutral genotype, then diversity still increases. Increasing diversity via mutation cannot be argued. It happens in every individual in every generation.
If the diversity is of no use to the "evolving" organism, but a disease process that portends its eventual demise then it is meaningless even to speak in terms of mutations increasing genetic diversity, as of course, to state the obvious, the reason genetic diversity matters so much to evolution is that it provides adaptive possibilities for the sake of survival, which deleterious and neutral alleles don't.
And how about the possibility that any supposed increase in evolutionarily useful genetic diversity through mutation is exceeded by the decrease in diversity that is brought about by various "Evolutionary Processes" that act on that population? These processes MAY exceed the useful mutation rate even to some great degree, could reduce the diversity significantly more than the mutations supposedly increase it. How would one be able to determine this and if you haven't determined this how can you pronounce so assertively that mutation does in fact increase diversity in any sense that is meaningful for evolution?
So you get, say, what, 1000 mutations in a population that don't abort, at 1000 loci, and then by migration or selection 200 of them separate from the parent population and develop a new "species." And I don't see what's wrong with calling this a "new phenotype" as that is how a new species is recognized, by this type that proliferates in the new population that differs from the parent population in some recognizable way, no?
Anyway, in the process of separating you have no idea how many thousands of alleles that existed in the original population may no longer occur in the new population -- or both populations for that matter -- at thousands of loci. How do you know whether these eliminations do or don't exceed the increase in alleles by mutation (and again evolutionally USEFUL alleles as this continues under dispute)?
And please note that I'm not talking only about NS, Natural Selection, but ALL the processes that isolate a population and develop a new type or "species" -- all the "Evolutionary Processes" that lead to the development of new types and to speciation. Certainly on many of the occasions such a split occurs there may be many other "hidden" forms of the same alleles that were eliminated still present, as in the case of the small beaks DBlevins brought up, but it's still an overall reduction in allelic diversity. Many many genes are affected by selection or migration etc. at one selection or other population reduction, many alleles, not just those involving one character such as beaks. Overall you have to agree that these processes DO reduce diversity -- the best that is possible is that they may manage not to reduce it too drastically but still genetic reduction is the overall effect and increase is never the result. [AbE: I still plan to consider Mammuthus' case of the cichlids so I hope too many don't jump on this particular post yet].
The question remains whether mutation adds allelic diversity in sufficient numbers OR quality to be a meaningful counteraction to the inexorable trend to genetic reduction brought about by the "Evolutionary Processes."
Mutation introduces changes that are called mistakes -- mistakes in DNA replication. MOST of them as Mammuthus just acknowleged, abort.
quote:
Most of them are neutral, but no matter. This highlights the real shift in your argument. You are no longer talking about decreasing diversity, but the old chestnut, "there aren't any/enough beneficial mutations".
Well, yes, it amounts to the same thing.
This message has been edited by Faith, 11-30-2005 10:51 PM

This message is a reply to:
 Message 134 by mark24, posted 11-30-2005 7:34 PM mark24 has replied

Replies to this message:
 Message 140 by mark24, posted 12-01-2005 4:16 AM Faith has not replied
 Message 142 by Mammuthus, posted 12-01-2005 5:19 AM Faith has not replied
 Message 152 by DBlevins, posted 12-01-2005 3:44 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 137 of 298 (264647)
12-01-2005 2:30 AM
Reply to: Message 63 by DBlevins
11-27-2005 9:26 PM


Re: A harder easy question
The predictable reduction in genetic diversity is the mechanism.
quote:
What predictable reduction in genetic diversity? Are you talking about creation? That sure isn't what evolution says is happenning. We do understand about mutations and natural selection?
Please review the posts by Mick, 28, Message 29 and Message 32 that agree that genetic diversity IS reduced by the processes we are discussing, so if you are arguing with me you are also arguing with him.
Variations don't exactly "build up." Whenever there is a variation in the phenotype there is a corresponding reduction in genetic diversity that allowed it to come to expression. They go together hand in hand, the reduction of genetic diversity and the production of a new phenotype. You don't get fancy breeds without the aggressive elimination of lots of genetic potentials, and the same thing happens in nature when you get a new type that is tightly designed to fit a niche and so on. It is only by eliminating other genetic possibilities that you get the new "species" and this being the case variation or "evolution" beyond the given genetic potentials of the original ancestral species is impossible.
quote:
Perhaps you forgot my explanation for this Faith? In that case here it is: From: Natural Limitation to Evolutionary Processes thread
Natural selection does NOT ALWAYS cause a reduction in variation because hidden variation is ALWAYS present in continuously varrying traits. Natural selection can INCREASE variation. How about an example of how this can come about, eh?

Suppose you have an environment that favors larger beaks in birds. We'll let + equal the gene for large beaks and - as the gene for small beaks. Because deeper beaks is determined by genes at many loci, a population of even large beaked birds + have some small beak genes -. Now when the birds with the smallest beaks die, alleles for the small beaks are removed from the breeding popuation. This may increase the frequency of the + gene at every loci, but because even the larger beaked birds have some - alleles, variation still remains. Reproduction shuffles these genes within the population and because + genes are more common, individuals in future generations will have more + alleles. Because the more + genes you have the deeper your beak, the population will show a shift to larger beaks, and the new generations biggest beaks will be bigger than the previous generation. If this continues the same thing happens again. The individuals with the biggest beaks will have beaks even larger than the previous generation. As you can see you have MORE variation. This process can even be reversed.
An example I have seen used is an experiment on oil content within seeds. The experiment conducted on corn showed that oil content could be increased, after 80 generations, beyond the initial oil content of 4-6%. The researchers were also able to reverse the process and select for low oil content instead. This showed that selection could INCREASE the initial range of variation.
(From Boyd and Silk, ibid, p. 74 with the citing found in the url below)
You are talking about what everybody knows happens in breeding programs, and it's basically the same thing Mick described in the OP as well only his example occurred by migration rather than selection. You can select more or less of anything and breed for it by selecting the varieties with more of what you want and eliminating those you don't want. The point is that in order to breed anything you have to ELIMINATE all the competing types, whether the oilier or the less oily it doesn't matter -- this is what I'm talking about, the REDUCTION OF GENETIC DIVERSITY which ALWAYS accompanies the production of new types.
And finally, where do you think our domestic dogs have come from? If they come from wolves and we SELECTED traits then of course you should be able to see that we do have MORE dog breeds and MORE variation in this species.
Clearly, DB, you are missing the point entirely. What we are talking about is that in order to produce new breeds, and "variation in the species" you have to ELIMINATE competing traits and that ALWAYS involves a reduction in genetic diversity.
It is hidden variation that is selected FOR in many situations of natural selection...
It is EXPRESSED variation that is selected for. Hidden variation is later expressed through reproduction/recombination.
What you seem to be overlooking is that you have eliminated some types from the population and that this involves a reduction in genetic diversity -- the fact that the same trait remains in another genetic form doesn't change the fact that you have eliminated it in its other forms. As I've been maintaining, as always, you produce new phenotypes BY reducing genetic diversity. You are going to get small beaks in the NEW population only along with the deeper beaks, as I believe you said, but no longer the simple small beaks of the parent population. These have been eliminated, reducing genetic possibilities/diversity.
I apologize if I misunderstood what you were saying. It seemed to me that you were talking about variation. Specifically a reduction in variation due to genetic drift/ NS.
I do think I percieve what you are saying and perhaps a misunderstanding about alleles that you might have. In your first post you talked about a reduction in alleles:
Migration out of a population leaves both the remaining populations genetically reduced. This is what happened with Darwin's Galapagos turtles. They are both likely to develop traits peculiar to themselves from their reduced allotment of alleles...
Yes, you're right. I tend to be thinking of the situation where the migrating population is much smaller so the genetic situation in the parent population may not be affected enough to change appreciably, but yes, if you remove any alleles from a population there will be a corresponding observable effect to some degree.
This is infact not the case. There is no genetic reduction, or reduced allotment of alleles, as if they are somehow reduced. Instead there is a shift in the frequency of alleles by selection working on the expressed alleles. This may or may not cause a reduction in the "FREQUENCY" of an allele, but that is because the frequency of a selected allele is increased.
Please review the posts by Mick (28, 29, 32) that I have mentioned, to see that he and I agree on this basic process of genetic reduction corresponding to the development of new types. The frequency refers to the fact that it occurs in more individuals in the new population, so that with respect to the defining characteristics of the new population there is always an increase in the frequency of the alleles for those characteristics or traits. But this particular genetic picture dominates in the new population, comes to characterize it as a new type or even a new "species" because of the elimination or sharp reduction of other alleles for those characteristics that existed in the parent population. In fact the parent population may also change in the direction of those alleles that did not leave with the migrants.
So if we see in our finches with small beaks that they are selected against, we still have a population of larger beaked birds that may have the small beak alleles.
Yes but meanwhile you HAVE eliminated the majority of the small beaks, and all of the small beaks of the type that characterized the parent population, which means you have reduced the genetic diversity.
In the case of a drastic reduction, such as a bottleneck the allele frequency may shift so much that the allele for small beaks doesn't exist in the population, but the number of alleles for that trait are still there, they may all be large beak alleles.
If they are all the same alleles, that shows a reduction in diversity as diversity implies different alleles for a trait. There is no longer the possibility of a small beak occurring in this new population if the allele for small beaks has been completely eliminated. This is a reduction in diversity.
To express this visually, suppose you have a population of birds that vary in beak size according to expressed alleles, as shown below (with - allele for small beaks and + allel for larger beaks). Now remember we are talking about continuouly varrying traits or multiple alleles affect a trait (such as height in humans.)
I've answered you DB.
This I think is the misperception you have about some reduction.
I believe I have shown that the misperception is yours. Again, please review the dialogue with Mick up to about message 36 or so.
As far as there being a reduction in variability. Variability is the "ability" to vary. What is stopping a mutation to act on or change one of the alleles, even if they were all + alleles? If a mutation acts or changes one of these alleles it will remain hidden and reshuffled among the population if it isn't detrimental to the reproduction of the species UNTIL selective forces act in such a way that this NOVEL ALLELE becomes expressed. This novel allele may or may not help the species to survive.
First, before we consider mutation, let's establish that you are wrong about my main point about the reduction of genetic diversity with the formation of new types or varieties or species through the reproductive segregation of a part of a population.
Mutation then emerges as the ONLY process that ADDS genetic material to the mix, and whether what it adds ever produces anything truly beneficial to the species, or whether such beneficial changes occur at a rate that can overcome the reduction effect of the migrating, selecting, isolating processes then becomes the question. It seems to me to be highly problematic to say the least, and that even with the most ideally positive input of mutation those processes nevertheless eventually inevitably produce a trend of reduced genetic diversity over time.
This message has been edited by Faith, 12-01-2005 02:33 AM
This message has been edited by Faith, 12-01-2005 10:12 AM

This message is a reply to:
 Message 63 by DBlevins, posted 11-27-2005 9:26 PM DBlevins has replied

Replies to this message:
 Message 153 by DBlevins, posted 12-01-2005 4:06 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 138 of 298 (264650)
12-01-2005 3:11 AM
Reply to: Message 82 by Mammuthus
11-28-2005 3:49 AM


I'm bumping this because Faith ignored these examples where genetic diversity did NOT decrease as a consequence of speciation since it occurred in sympatry...and not to pick on Faith, nobody else picked up on these examples either
Isn't sympatry just a version of reproductive isolation between members of the same species? If so, this isn't a different example and of course genetic diversity decreases as the genes of the parent population are left behind and fewer genes are maximized in the new population. If it is, I will try to get how it's different.
Ok, here come the cichlids,
Note, going from the arguement in the OP, why do cichlids form populations/species that no longer exchange genetic information with one another even though the populations occur in the same lakes i.e. sympatric speciation? This is a nice example of macroevolution that is observable at the genetic level...what is the difference between what we observe between cichlid species as opposed to within cichlid populations? (Note: most of these articles are open access and anyone who want to, can read them)
OK, I'll have to comment as I go to keep on top of this. So far this sounds like the wrong question. Why it occurs is not important, as it is just another case of the situation we are discussing on this thread and this situation comes about by many processes. So this is apparently another one of the processes that isolate populations of the same species from one another reproductively. Mick's examples were of geographic isolation. Whatever isolates the populations, the same mechanisms are at work: each population has a portion of the original gene pool and expresses it phenotypically to the exclusion of the genetic types in the other pool. So, as with Mick's chipmunks, you get two separate varieties of the same species that either have no opportunity, no ability or no interest in interbreeding. And in all these cases genetic diversity IS reduced as in order for the differences in traits to emerge, the alleles for the other forms of those traits must have been eliminated or significantly reduced in the new population or "species."
BACKGROUND: The adaptive radiations of cichlid fishes in East Africa are well known for their spectacular diversity and their astonishingly fast rates of speciation. About 80% of all 2,500 cichlid species in East Africa, and virtually all cichlid species from Lakes Victoria (approximately 500 species) and Malawi (approximately 1,000 species) are haplochromines. Here, we present the most extensive phylogenetic and phylogeographic analysis so far that includes about 100 species and is based on about 2,000 bp of the mitochondrial DNA. RESULTS: Our analyses revealed that all haplochromine lineages are ultimately derived from Lake Tanganyika endemics. We find that the three most ancestral lineages of the haplochromines sensu lato are relatively species poor, albeit widely distributed in Africa, whereas a fourth newly defined lineage - the 'modern haplochromines' - contains an unparalleled diversity that makes up more than 7% of the worlds' approximately 25,000 teleost species. The modern haplochromines' ancestor, most likely a riverine generalist, repeatedly gave rise to similar ecomorphs now found in several of the species flocks. Also, the Tanganyikan Tropheini are derived from that riverine ancestor suggesting that they successfully re-colonized Lake Tanganyika and speciated in parallel to an already established cichlid adaptive radiation. In contrast to most other known examples of adaptive radiations, these generalist ancestors were derived from highly diverse and specialized endemics from Lake Tanganyika. A reconstruction of life-history traits revealed that in an ancestral lineage leading to the modern haplochromines the characteristic egg-spots on anal fins of male individuals evolved.
Or were possibly recessive until the dominant forms were eliminated and allowed them to come to expression in the phenotype. Or were produced by genetic drift or whatever, again all processes that involve the reduction of genetic diversity in the service of developing new phenotypes, traits, characteristics, "species."
CONCLUSION: We conclude that Lake Tanganyika is the geographic and genetic cradle of all haplochromine lineages. In the ancestors of the replicate adaptive radiations of the 'modern haplochromines', behavioral (maternal mouthbrooding), morphological (egg-spots) and sexually selected (color polymorphism) key-innovations arose. These might be - together with the ecological opportunity that the habitat diversity of the large lakes provides - responsible for their evolutionary success and their propensity for explosive speciation.
A "propensity for explosive speciation" simply suggests to me that they have a propensity to split into smaller populations that stop breeding with the parent population, for whatever reason -- a habit of migration, or picky sexual selection or whatever? (Fish are sexual, sort of anyway, right?) In any case I see no difference in teh genetic situation from the example Mick gave or any situation produced by the Evolutionary Processes (migration, genetic drift, natural selection, sexual selection, founder effect, bottleneck, and so on -- also including mutation but that's the exception in that it increases alleles and genetic diversity and is now starting to be discussed on this thread as the separate process it is). You are giving new examples but there's no difference in the genetic picture that I can see -- wherever you have a new population started by some individuals from the parent population you have a genetically reduced population with new phenotypic expressions that differentiate it from the parent population.
Here are some bat references,
Taxonomic relationships within the Old World fruit bat genus, Cynopterus, have been equivocal for the better part of a century. While nomenclature has been revised multiple times on the basis of phenotypic characters, evolutionary relationships among taxa representing the entire geographic range of the genus have not been determined. We used mitochondrial DNA sequence data to infer phylogenetic relationships among the three most broadly distributed members of the genus: C. brachyotis, C. horsfieldi, and C. sphinx, and to assess whether C. brachyotis represents a single widespread species, or a complex of distinct lineages. Results clearly indicate that C. brachyotis is a complex of lineages. C. sphinx and C. horsfieldi haplotypes formed monophyletic groups nested within the C. brachyotis species complex. We identified six divergent mitochondrial lineages that are currently referred to C. brachyotis. Lineages from India, Myanmar, Sulawesi, and the Philippines are geographically well-defined, while in Malaysia two lineages, designated Sunda and Forest, are broadly sympatric and may be ecologically distinct. Demographic analyses of the Sunda and Forest lineages suggest strikingly different population histories, including a recent and rapid range expansion in the Sunda lineage, possibly associated with changes in sea levels during the Pleistocene. The resolution of the taxonomic issues raised in this study awaits combined analysis of morphometric characters and molecular data. However, since both the Indian and Malaysian Forest C. brachyotis lineages are apparently ecologically restricted to increasingly fragmented forest habitat, we suggest that reevaluation of the conservation status of populations in these regions should be an immediate goal.
I'm not sure what this focus on lineages is intended to prove, but as with the above, I expect variation within species and nothing about it contradicts creationist expectations so if you think it does I hope you will be more specific.
This message has been edited by Faith, 12-01-2005 03:18 AM

This message is a reply to:
 Message 82 by Mammuthus, posted 11-28-2005 3:49 AM Mammuthus has replied

Replies to this message:
 Message 141 by Mammuthus, posted 12-01-2005 4:28 AM Faith has replied

  
Mammuthus
Member (Idle past 6505 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 139 of 298 (264654)
12-01-2005 3:56 AM
Reply to: Message 120 by Faith
11-30-2005 11:25 AM


Re: Trying to get reoriented so I won't give up
quote:
Hybridization, sexual recombination etc. Not a genuine increase according to a creationist, simply a way the trend to reduction is masked in a large gene pool.
But that is not what I am talking about. I am talking about NEW mutations. Also recombination can produce large scale mutations that never existed before since it does not always work properly either. My point about hybridization is that speciation does not require reduction in genetic diversity.
quote:
According to my conjectures, it is in species that are threatened with extinction where this trend of genetic reduction reaches its final extreme, that's why it is noted at that point, and those extremes do tend to be where "speciation" has recently occurred, no? In any case, I am convinced those extremes prove the overall trend, "the way of all flesh" as it were.
I mean something very different. A species on the verge of extinction has been reduced to a very small number of breeding individuals. Thus, the population will be very homogeneous. And small numbers and lack of diversity (particularly of the genes controlling the immune system) puts the species at risk of complete collapse. A bottleneck during speciation does not have to be so extreme...a very diverse and large population could be cut in half...both halves would still have a lot of diversity and could still speciate...like in cichlids.
quote:
I am certain there is a genetic allotment so your flat assertion that it's been disproved doesn't deter me
I made a flat assertion because you complained that I was going over your head. I could very easily link you to the scientific studies that refute the concept of genetic allotment. It is not a new find. Denying it is simply denying reality.
quote:
It is a terrible handicap to have no experience of talking biology with a nonbiologist. I don't know if it's possible to overcome that.
But I guess it is fun to try or we would not be posting to each other in this thread
quote:
Thanks for the acknowledgment that most mutations are unsuccessful. How sure are you that that leaves enough useful ones to counteract the genetic reduction effects of selection, migration, bottleneck and so on? What kind of data/statistics could even be available about this?
Because we observe mutations in each generation that have not been aborted. As I said, every single one of us has novel mutations that do not occur in our parents. Have you heard of PCR the polymerase chain reaction where you can amplify DNA from a single copy to millions in a test tube? Even here, you can find polymerase errors in your sequences due to its lack of fidelity. Companies spend big bucks trying to make error free polymerases....our bodies don't.
I also want to point out since you have mentioned this in two posts now, migration does not reduce genetic diversity. In fact, migration is a good way to keep gene flow constant over distant populations. Two groups will not diverge if they keep migrating into each other...migration is a great way to reverse trends towards speciation.
quote:
Thanks for keeping your post short.
No problem...I also have limited time (should be working on grants )
and mick and others have posts that are worth you time as well...so I will try to avoid excessively long posts.

This message is a reply to:
 Message 120 by Faith, posted 11-30-2005 11:25 AM Faith has not replied

  
mark24
Member (Idle past 5225 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 140 of 298 (264655)
12-01-2005 4:16 AM
Reply to: Message 136 by Faith
11-30-2005 9:56 PM


Re: Trying to get reoriented so I won't give up
Faith,
If the diversity is of no use to the "evolving" organism, but a disease process that portends its eventual demise then it is meaningless even to speak in terms of mutations increasing genetic diversity,
No, it is meaningless to speak of genetic diversity representing a block to evolution. More genetic diversity does not necessarily mean more beneficial mutations.
Time to call a spade a spade, Faith. Your issue is not with diversity, but beneficial mutations.
Mark

There are 10 kinds of people in this world; those that understand binary, & those that don't

This message is a reply to:
 Message 136 by Faith, posted 11-30-2005 9:56 PM Faith has not replied

Replies to this message:
 Message 143 by Mammuthus, posted 12-01-2005 5:22 AM mark24 has not replied

  
Mammuthus
Member (Idle past 6505 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 141 of 298 (264656)
12-01-2005 4:28 AM
Reply to: Message 138 by Faith
12-01-2005 3:11 AM


quote:
Isn't sympatry just a version of reproductive isolation between members of the same species? If so, this isn't a different example and of course genetic diversity decreases as the genes of the parent population are left behind and fewer genes are maximized in the new population. If it is, I will try to get how it's different.
Speciation in sympatry leads to reproductive isolation without any physical barrier to gene flow being involved. It does not necessarily lead to reduction in genetic diversity if the breeding population of the two groups is the same when speciation occurs. Also, once speciation occurs, mutation and evolution do not stop...even after a bottleneck, over time you might find the smaller population has greater diversity than the original larger population.In fact, if two species hybridize and the resultant hybrid can no longer breed with either parent species, then speciation has lead to a dramatic increase in genetic diversity in the new species compared to the separate original species.
quote:
Whatever isolates the populations, the same mechanisms are at work: each population has a portion of the original gene pool and expresses it phenotypically to the exclusion of the genetic types in the other pool. So, as with Mick's chipmunks, you get two separate varieties of the same species that either have no opportunity, no ability or no interest in interbreeding. And in all these cases genetic diversity IS reduced as in order for the differences in traits to emerge, the alleles for the other forms of those traits must have been eliminated or significantly reduced in the new population or "species."
Interesting, but you seem to be admitting that speciation can happen. Your statement is largely correct except for the expressing of phenotypes that are present in the new population part. The new phenotypes evolve in separation. At the moment when two populations are separated, they are just a subset of the original population. They may have genotype/phenotypes that are present in both populations but the frequencies are different. It is only after time that they will start to adapt and diverge...the absence of gene flow between the two populations will insure that they start becoming phenotypically divergent.
How is this different than say the processes that separate bears from dogs..elephants from manatees?
quote:
Or were possibly recessive until the dominant forms were eliminated and allowed them to come to expression in the phenotype. Or were produced by genetic drift or whatever, again all processes that involve the reduction of genetic diversity in the service of developing new phenotypes, traits, characteristics, "species."
This again makes no sense. If there are 8 blue balls and 2 red ball in a population and one red ball goes on to found a new population, the red phenotype is not surpressed in the old population. It is at a lower frequency. After a few hundred generations, maybe there are no red balls left in the original population by chance or selection..but the red ball population has grown and has new mutants, say purple. Now you have two populations, one all blue, and one with red and purple...this is what we observe. Not that if you are suddenly isolated you just grow a new phenotype. What you are proposing is basically Lamarkism which was refuted long ago.
quote:
You are giving new examples but there's no difference in the genetic picture that I can see --
This is the point...there is no difference between generation of a new population, species, genus, family, order etc. the process is the same. The only difference is the length of time involved. Two closely related species may be equally genetically diverse because since they speciated, they have built up genetic diversity after the reduction. This is directly observable. This is what we see. Evolution is change over time..the more time, the more change..it is exactly what we see looking at genetics and and to some extent, morphology, no matter what taxanomic level we are considering.
quote:
I'm not sure what this focus on lineages is intended to prove, but as with the above, I expect variation within species and nothing about it contradicts creationist expectations so if you think it does I hope you will be more specific.
It contradicts creationist expectations because in all cases it contradicts the concept of immutable kinds. The fact that every individual is born with novel mutations contradicts "genetic allotment". Everything from the biochemistry of DNA, RNA and proteins to the study of mutations segregating in families, groups, populations, species, genera, etc. demonstrates that evolution occurs. Where it cannot be directly measured (over millions of years) it leaves behind footprints exactly like those we observe today. Even ancient DNA lets us directly observe the process over vast time spans.
What creationists fail to do is show how the different levels of divergence in mick's example, or any example are different biologically i.e. what is the difference between dogs and cats diverging as opposed to house cats from cheetah's? Every piece of evidence ever gathered says there is no difference in the underlying process. Creationism is the denial of this evidence. Creationism denies that mutations increase diversity even within a species. But other than arguments about contradicting faith or personal beliefs and asthetics, creationism does this with no supporting evidence and loads of evidence that contradicts it.

This message is a reply to:
 Message 138 by Faith, posted 12-01-2005 3:11 AM Faith has replied

Replies to this message:
 Message 146 by Faith, posted 12-01-2005 11:45 AM Mammuthus has replied

  
Mammuthus
Member (Idle past 6505 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 142 of 298 (264660)
12-01-2005 5:19 AM
Reply to: Message 136 by Faith
11-30-2005 9:56 PM


Re: Trying to get reoriented so I won't give up
quote:
Mutation introduces changes that are called mistakes -- mistakes in DNA replication. MOST of them as Mammuthus just acknowleged, abort
I don't want to draw the thread off topic but I was grossly oversimplifying here. I was talking about mutations that affect phenotype. Most DNA is non-coding so most mutations are neutral or slightly deleterious. But I did not want to drag the entire topic into mutation analysis

This message is a reply to:
 Message 136 by Faith, posted 11-30-2005 9:56 PM Faith has not replied

  
Mammuthus
Member (Idle past 6505 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 143 of 298 (264661)
12-01-2005 5:22 AM
Reply to: Message 140 by mark24
12-01-2005 4:16 AM


Re: Trying to get reoriented so I won't give up
Hi Mark,
maybe it would be worthwhile to start a thread on mutations for Faith? I am having enough trouble keeping up these days and am heading off to give a lecture next week so I would like to leave it in your hands
Cheers,
M

This message is a reply to:
 Message 140 by mark24, posted 12-01-2005 4:16 AM mark24 has not replied

  
Mammuthus
Member (Idle past 6505 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 144 of 298 (264663)
12-01-2005 5:29 AM
Reply to: Message 128 by mick
11-30-2005 2:09 PM


Re: Snowing under
Hi mick
Let me know if any of my posts (aside from this one maybe) contribute to derailing the thread...even if the topic of the derailment is interesting. Feel free to boot me out of it. I rather see progress on the topic than contribute since I have been trying for years to get a creationist to engage in exactly this topic. Faith has taken it up so I don't want her to leave in frustration because of distractions.
cheers,M

This message is a reply to:
 Message 128 by mick, posted 11-30-2005 2:09 PM mick has not replied

  
Brad McFall
Member (Idle past 5062 days)
Posts: 3428
From: Ithaca,NY, USA
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Message 145 of 298 (264680)
12-01-2005 8:11 AM
Reply to: Message 133 by mick
11-30-2005 5:47 PM


REsearch of Will Provine
Howarth & Marino Lab Group: Data
quote:
Provine, W. B. 1971. The origins of theoretical population genetics. University of Chicago Press, Chicago.
Mayr, E. and W. B. Provine, eds. 1980. The evolutionary synthesis. Harvard University Press, Cambridge, MA.
Provine, W. B. 1986. Sewall Wright and evolutionary biology. University of Chicago Press, Chicago.
Provine, W. B., ed. 1986. Evolution: Selected papers by Sewall Wright. University of Chicago Press, Chicago.
Provine, W. B. 1986. Geneticists and race. American Zoologist 26:857-887.
Provine, W. B. 1989. Progress in evolution and meaning in life. Pp. 49-74, In: M. Nitecki, ed., Evolutionary Progress. University of Chicago Press, Chicago.
He wrote, "Sewall Wright and evolutionary biology" when he was supposed to have been my Cornell apointed "mentor" for the College Scholar Program at CU where a select number of undergrads graduate without a major writing a thesis instead. I was writing a thesis on the evolution of worm snakes. He failed to come through. He still did not two decades later either. This year he said that he is writing a book on drift claiming to show that it does not occur in the Wrightian, "or any other sense." He said he aired the idea, I guess at Harvard, already, where Richard Lewontin "defended" Will (Will was Richard's grad student in the 60s) during the approach of those dreaded 'post-docs' during some kind of Q&A.
If you read the 86 book and Shipley's "Cause and Correlation in Biology"
http://www.callisto.si.usherb.ca:8080/bshipley/my%20book.htm
(the whole thing is free online(ok it looks like opportunity cost is $5)
you will understand completely where/what I am trying to say, unless there are a few asides about Gould's ideas, as the only real issue that instead got me hospitalized in the 80s was the lack of the applicability of econometric structure equations to biological praxis Shipley transferred in 2000 from work in the late 80s and early 90s in the US. I need to know if Will continues to discount this angle and it is easy enough to see how he might in his philosophical approach to Wright in SWEB1986 else the problem is with the so-called "adaptive hardening" post synthesis. I stress adaptibility while others seem to find competition more compelling. This can also re-frame the Wright-Fisher difference but let me not go when I am not ready. Later...
This message has been edited by Brad McFall, 12-01-2005 08:16 AM

This message is a reply to:
 Message 133 by mick, posted 11-30-2005 5:47 PM mick has not replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 146 of 298 (264737)
12-01-2005 11:45 AM
Reply to: Message 141 by Mammuthus
12-01-2005 4:28 AM


Isn't sympatry just a version of reproductive isolation between members of the same species? If so, this isn't a different example and of course genetic diversity decreases as the genes of the parent population are left behind and fewer genes are maximized in the new population. If it is, I will try to get how it's different.
Speciation in sympatry leads to reproductive isolation without any physical barrier to gene flow being involved. It does not necessarily lead to reduction in genetic diversity if the breeding population of the two groups is the same when speciation occurs. Also, once speciation occurs, mutation and evolution do not stop...even after a bottleneck, over time you might find the smaller population has greater diversity than the original larger population.
MIGHT. Sounds awfully conjectural, and I'm trying to get across that I'm talking about an overall trend to reduction, despite the fact that any particular case may show an increase.
In fact, if two species hybridize and the resultant hybrid can no longer breed with either parent species, then speciation has lead to a dramatic increase in genetic diversity in the new species compared to the separate original species.
Hybridization does add alleles so it's not the same kind of process as the others which merely reduce alleles in order to produce new types, and focusing on it can confuse this discussion. My point is that the MAJORITY of the processes that lead to speciation (selection, migration, bottleneck etc) subtract alleles. Perhaps that's a clearer way of putting it. Mutation and hybridization or sexual recombination add them, but the others subtract. The question becomes whether, overall, in the whole evolutionary picture across all species, the factors that increase outstrip the factors that decrease or vice versa.
Whatever isolates the populations, the same mechanisms are at work: each population has a portion of the original gene pool and expresses it phenotypically to the exclusion of the genetic types in the other pool. So, as with Mick's chipmunks, you get two separate varieties of the same species that either have no opportunity, no ability or no interest in interbreeding. And in all these cases genetic diversity IS reduced as in order for the differences in traits to emerge, the alleles for the other forms of those traits must have been eliminated or significantly reduced in the new population or "species."
quote:
Interesting, but you seem to be admitting that speciation can happen.
What you CALL speciation DOES happen ALL THE TIME, but a creationist does not regard it as anything more than variation within a species. LOTS of variations/breeds/subspecies occur all the time, which I've been saying from the beginning, but there is a limit to this process and my whole point here is to suggest that that limit is the fact that the overall trend of the "evolutionary processes" is a reduction in alleles and in genetic diversity which ultimately has an end point, even at its extreme the extinction of the species, and does NOT lead in the direction of genetic increase EXCEPT in particular, less frequent, and temporary cases when hybridization or mutation can be shown to bring this about -- and I'd like to leave these for a separate discussion as they only muddy up the point about the overall genetic reduction that otherwise always accompanies the formation of new "species" (breeds, types, varieties, subspecies).
Yur statement is largely correct except for the expressing of phenotypes that are present in the new population part. The new phenotypes evolve in separation. At the moment when two populations are separated, they are just a subset of the original population. They may have genotype/phenotypes that are present in both populations but the frequencies are different. It is only after time that they will start to adapt and diverge...the absence of gene flow between the two populations will insure that they start becoming phenotypically divergent.
Yes and it is true that I tend to have in mind the dramatic cases where whole rafts of alleles have been completely eliminated from the new population, and the fact that some remain at all, in new frequencies, does mean that diversity itself is not reduced. Still this does it seems to me represent the trend I'm talking about only less dramatically. That is, getting a new phenotype does always involve the REMOVAL of the alleles for other phenotypes and the more this process of splitting continues the greater the reduction. It does not involve an addition (again, as I understand it, addition of alleles only happens with mutation and hybridization or sexual recombination and I'm trying to treat these as separate processes.)
How is this different than say the processes that separate bears from dogs..elephants from manatees?
If there is IN FACT genetic descent from one to the other the processes ARE the same, but while I could see that elephants and manatees might have that relationship (without knowing the genetics involved of course), I can't see it between bears and dogs. Bears and raccoons, yes. Dogs and wolves yes. (Perhaps hyenas are not related as some have suggested earlier in the thread, but subjectively I would want to include them with dogs). Admittedly this is a subjective categorization but while there may be no evidence for it, there is no evidence against it either. Evolution assumes genetic descent partly because there has not been shown any stopping point in the evolutionary processes under discussion but creationists deny it and there is no evidence for it. All you have is the observed mechanisms of species variation we are discussing, and again, the overall trend in the edevelopment of such new types or variations or breeds is to genetic reduction (again, for the purpose of highlighting this fact leaving out mutation and hybridization)which hardly supports evolution. And again, the very possibility of evolution apparently depends completely on mutation and the other additive processes as the majority of what have been called evolutionary processes only subtract genetic potentials. And again again, I'm trying to keep the focus on these subtracting processes in this thread.
Or were possibly recessive until the dominant forms were eliminated and allowed them to come to expression in the phenotype. Or were produced by genetic drift or whatever, again all processes that involve the reduction of genetic diversity in the service of developing new phenotypes, traits, characteristics, "species."
This again makes no sense. If there are 8 blue balls and 2 red ball in a population and one red ball goes on to found a new population, the red phenotype is not surpressed in the old population.
I don't see how the term "suppression" came into this at this point, but I think maybe the general point got discussed above.
It is at a lower frequency. After a few hundred generations, maybe there are no red balls left in the original population by chance or selection..but the red ball population has grown and has new mutants, say purple.
Please do not introduce the idea of mutation in this discussion. For the sake of clarity I need to keep the discussion confined to the genetic situation given at the time of the split of the populations. If one red ball creates a new population it will be a population of red balls. Since one red ball stays behind in the old population it will now occur at this new reduced frequency. But it WILL be a REDUCED frequency of red balls as one of the two has left. Therefore the blue balls will dominate even MORE in the old population than they did before the split. It will be a BLUER parent population. And this will have occurred because of the REMOVAL of a red ball. The point is always that the removal or elimination of some genetic potential is the WAY new types emerge through these particular processes [selection, (natural, domestic or sexual), migration, bottleneck etc.] what you call "speciation." And again, this is to leave out mutation and hybridization for the moment, simply in order to demonstrate that the process I'm focusing on is a process of removal or reduction, and leaving out hybridization and mutation it is ALWAYS a process of removal or reduction.
Now you have two populations, one all blue, and one with red and purple...this is what we observe. Not that if you are suddenly isolated you just grow a new phenotype. What you are proposing is basically Lamarkism which was refuted long ago.
See above. I don't know how you are reading me to be saying we're "growing a new phenotype." And again, please leave out mutation in order that these processes I'm trying to highlight can be seen clearly as the reducing processes they are. Which gives us a BLUER parent population (purple but less red-purple and more blue-purple than before) and an all-red new population.
You are giving new examples but there's no difference in the genetic picture that I can see --
This is the point...there is no difference between generation of a new population, species, genus, family, order etc. the process is the same. The only difference is the length of time involved.
This is simply evolutionist faith, an assumption that is taken for granted but has not been proved. But if there is an overall reduction in genetic potential or diversity with these processes (selection, migration, population reduction and reduction of breeding etc) that lead to "speciation," then there is a natural end point to evolution and that end point is the limits of variation/subspecies formation possible in all directions within the Kind beyond which only extinction is possible.
Two closely related species may be equally genetically diverse because since they speciated, they have built up genetic diversity after the reduction. This is directly observable. This is what we see.
Are you talking about hybridization or what? What exactly is it you are "seeing?" This does get into the other subject I've been trying to keep separate, mutation and other additive processes like hybridization, and crashfrog also claimed that even the cheetah shows a buildup of such diversity. I'm afraid of confusing the topic by getting into this, but I really do not know what it is you think you are actually SEEING. The cheetah is about as genetically compromised as you can get, so if it has been accumulating diversity it isn't the greatest case for evolution anyway.
Evolution is change over time..the more time, the more change..it is exactly what we see looking at genetics and and to some extent, morphology, no matter what taxanomic level we are considering.
Creationists answer that all the changes that are seen are limited by the Kind, and I'm trying to suggest a major mechanism how that may happen. Evolutionists always answer that they can't prove their belief that it is open-ended because of the time factor, but all the observations that have been made suggest nothing more than that variation is possible and in fact may be highly frequent, within a species or Kind without implying anything beyond the species or Kind.
I'm not sure what this focus on lineages is intended to prove, but as with the above, I expect variation within species and nothing about it contradicts creationist expectations so if you think it does I hope you will be more specific.
It contradicts creationist expectations because in all cases it contradicts the concept of immutable kinds.
Not at all. All that has happened is that evolutions have been ASSUMING an openended process, but they can't demonstrate it.
The fact that every individual is born with novel mutations contradicts "genetic allotment".
Now we are getting into mutations and I want to think about that separately.
Everything from the biochemistry of DNA, RNA and proteins to the study of mutations segregating in families, groups, populations, species, genera, etc. demonstrates that evolution occurs. Where it cannot be directly measured (over millions of years) it leaves behind footprints exactly like those we observe today. Even ancient DNA lets us directly observe the process over vast time spans.
I see, so I guess I don't have to bother thinking about the selection processes that show this to be highly unlikely. In any case, this is just a statement of faith, an abstraction that needs serious unpacking if I'm going to understand any of it.
What creationists fail to do is show how the different levels of divergence in mick's example, or any example are different biologically i.e. what is the difference between dogs and cats diverging as opposed to house cats from cheetah's?
Evolutionists have never shown that there is any genetic connection between dogs and cats. You simply assume it. No problem with cats though. All cats are of one Kind. A cheetah is a cat related to the house cat. They both diverged from earlier cats, which diverged from the original Cat.
Every piece of evidence ever gathered says there is no difference in the underlying process.
But every piece of evidence only demonstrates what everybody knows about breeding, and nothing whatever that shows you can get anything but a dog from a dog.
Creationism is the denial of this evidence.
Not at all, it is a different understanding of the evidence.
Creationism denies that mutations increase diversity even within a species.
I haven't yet seen this convincingly demonstrated at all. What diversity there is appears to be useless evolutionarily anyway, and when the reducing processes like selection get to work on it in order to speciate it you are reducing genetic diversity anyway as I've been saying, so you still have to show that the increasing factors outdo the decreasing factors.
But other than arguments about contradicting faith or personal beliefs and asthetics, creationism does this with no supporting evidence and loads of evidence that contradicts it.
There is very little evidence that can't be explained in creationist terms without any reference whatever to faith or belief etc.
This message has been edited by Faith, 12-01-2005 11:46 AM

This message is a reply to:
 Message 141 by Mammuthus, posted 12-01-2005 4:28 AM Mammuthus has replied

Replies to this message:
 Message 156 by Mammuthus, posted 12-02-2005 4:09 AM Faith has replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 147 of 298 (264748)
12-01-2005 12:43 PM
Reply to: Message 103 by Modulous
11-29-2005 3:45 AM


Re: They are still Tamias....
Are you saying that massive morpholigical change would still not be macroevolution,...
Yes. It really isn't all that massive anyway. Size differences can be huge, particular features may be reduced or exaggerated, and all be the same species. I have no problem considering the sabre-toothed tiger a cousin of the tabby.
... and the deciding factor is behaviour?
No, I haven't gone that far, it simply struck me that the behaviors that we associate with existing species quite strikingly continue in the most bizarre breeds, so that they may in fact be a clue to a Kind -- but there may also be others.
What if the brain changed as part of the morphological change?
I would expect that to occur to some extent along with the other bodily changes. But I wouldn't expect it to change far enough to change some defining characteristics of the species (and I do think the behaviors I listed MAY be that).

This message is a reply to:
 Message 103 by Modulous, posted 11-29-2005 3:45 AM Modulous has replied

Replies to this message:
 Message 148 by Modulous, posted 12-01-2005 12:59 PM Faith has replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 148 of 298 (264754)
12-01-2005 12:59 PM
Reply to: Message 147 by Faith
12-01-2005 12:43 PM


They are still dogs....
Yes. It really isn't all that massive anyway
The difference between a rabbit and a dog isn't all that much? If you think behaviour gives us clues towards kinds, its an interesting idea. We'd need to develop some criteria so that we can test it.

This message is a reply to:
 Message 147 by Faith, posted 12-01-2005 12:43 PM Faith has replied

Replies to this message:
 Message 149 by Faith, posted 12-01-2005 1:03 PM Modulous has replied

  
Faith 
Suspended Member (Idle past 1474 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 149 of 298 (264755)
12-01-2005 1:03 PM
Reply to: Message 148 by Modulous
12-01-2005 12:59 PM


Re: They are still dogs....
The difference between a rabbit and a dog isn't all that much?
I thought you were talking about BREEDING such morphological changes so that we KNOW that they are inherited, not comparing two different Kinds whose supposed genetic relatedness is only a fiction of the evolutionist's imagination.
If you think behaviour gives us clues towards kinds, its an interesting idea. We'd need to develop some criteria so that we can test it.
I gave a list of behaviors I associate with dogs and cats. Feel free to add or subtract or modify. The only test I can think of would involve breeding animals with an eye to eradicating those behaviors.
AbE: Certainly you can modify them, exaggerate or diminish them, but get me a dog that eats rabbit food and uses a litter box, or a cat that wags its tail and barks at strangers and I'll be convinced.
This message has been edited by Faith, 12-01-2005 01:08 PM

This message is a reply to:
 Message 148 by Modulous, posted 12-01-2005 12:59 PM Modulous has replied

Replies to this message:
 Message 150 by Modulous, posted 12-01-2005 1:11 PM Faith has replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 150 of 298 (264757)
12-01-2005 1:11 PM
Reply to: Message 149 by Faith
12-01-2005 1:03 PM


Re: They are still dogs....
I thought you were talking about BREEDING such morphological changes so that we KNOW that they are inherited, not comparing two different Kinds whose supposed genetic relatedness is only a fiction of the evolutionist's imagination.
I was referring to the comment:
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
I think that is pretty massive morphological change.
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
These characteristics aren't unique to dogs. Do all characteristics have to be present, or just one? I see some interesting discussion possible here, worthy of its own topic perhaps?

This message is a reply to:
 Message 149 by Faith, posted 12-01-2005 1:03 PM Faith has replied

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 Message 151 by Faith, posted 12-01-2005 2:07 PM Modulous has not replied

  
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