Message 181 of 1034 (692155) 02-28-2013 10:22 AM

Reply to: Message 178 by Faith 02-28-2013 9:44 AM

No generating variation is not evolution. Evolution is variation + selection. Those processes need not be simultaneous. The end result over long periods can be speciation, but not every variation results in the kind of survival dominance that produces speciation.

You are still not quite describing how evolution actually works.

Selection works only on traits that affect fitness in a given environment. Traits that do not affect fitness can still be passed on to descendents. However, some of those traits might be selected for if the environment changes.

Selection has not produced a homogeneous population of human beings in the last few thousand years.

Let's be more specific about what "blending" means.

Only some individuals would have that non-beneficial and non deleterious change. Phenotype changes don't magically get distributed to entire populations unless they improve fitness to a degree that substantially punishes individuals not having the trait by making it too competitively hard for them to bear young. Only the mutant's descendents can get a particular mutation.

And if conditions change, or if some part of the species enters an environment in which conditions favor that particular phenotype, then we can get speciation due to the separation. In that case both species will exist and will be equally diverse to the pre-mutation population. But speciation need not begin at the same point in time at which the mutation appears.

There is only one species of humans with some diversity. There are also 8 species of bears and grizzlies are just one type of brown bear. Some of the species of bear can interbreed. So just which grouping represents more diversity?

Evolution can produce new species, but the evolution is slow, and involves processes that are not themselves evolution.

Message 182 of 1034 (692159) 02-28-2013 10:47 AM

Reply to: Message 155 by Faith 02-27-2013 7:41 PM

Where did you back this claim with evidence?

Message 183 of 1034 (692160) 02-28-2013 10:53 AM

Reply to: Message 160 by Faith 02-27-2013 8:31 PM

The vast majority of mutations do not occur in genes, promoters, or transcription factors so I would say that the vast majority are neutral. Of the mutations that change protein sequences I would think that a fair amount are deleterious, much more so than those that occur in non-coding and non-regulatory DNA. We can also see negative selection removing these mutations by comparing the genomes of species. When we do so we find something very interesting. We find that mutations which do not change the amino acid sequence of proteins are more common in a gene than those that do change the amino acid sequence. This tells us that selection is removing deleterious mutations.

This doesn't change the fact that the DNA differences seen between species contain mutations that are beneficial to each species. We KNOW that they exist because we can see them. We can find them.

Why wouldn't selection remove them just as selection has been removing deleterious mutations since evolution started?

Message 184 of 1034 (692161) 02-28-2013 10:58 AM

Reply to: Message 176 by Faith 02-28-2013 9:28 AM

They are being selected for, and this is shown by comparing our genomes to that of other apes. We can find patterns of positive and negative selection. I even highlighted evidence of positive selection in the case of the mc1r gene in pocket mice. Remember that?

If alleles are flowing in and selection is changing allele frequencies then you have change in a species over time, otherwise known as evolution.

The phenotypic change shows up in the first organism that carries the mutation. The first pocket mouse with the mutation conferring black fur had black fur.

Message 185 of 1034 (692162) 02-28-2013 11:00 AM

Reply to: Message 179 by Percy 02-28-2013 10:02 AM

I know that, but if they are being selected and mutation is continuing to add to the gene pool you aren't getting a delineated recognizable species such as we see IN REALITY both in the wild and in breeding. This is all just some abstract idea that has nothing to do with what really happens. I don't know what you would get in this scenario but it's something blurry and constantly changing, NOT an identifiable new species which is what happens IN REALITY.

See above. This is all theory gone bonkers, it has nothing to do with reality.

Is evolution about forming new SPECIES or about the myriad of different traits that show up in all populations? New traits show up in individuals in my scenario too, WITHOUT mutations.

But to GET that new species the traits have to be SELECTED AND ISOLATED. That's my point. The traits that constantly crop up in individuals in any fairly genetically diverse population, whether by mutation or by what I think it is, simply new combinations of existing alleles, do not constitute a new SPECIES unless selected, isolated and worked through the entire new gene pool. And THAT happens only when all the alleles for OTHER traits are suppressed, reduced, or eliminated = REDUCED GENETIC DIVERSITY REQUIRED TO FORM A NEW SPECIES.

So? Should happen a lot in my scenario that you get new "species" from new mixes of old alleles. If you want to insist on mutations then realize that mutations are only going to keep delaying the formation of an identifiable new species by interfering with the gene pool from which the species is formed. But that isn't what happens in reality.

So? I would assume there were lots of variations in the ancient world too, which on my system would be formed from new traits built from new combinations of alleles that are brought to expression by selection and isolation just as they are in living species today, not requiring mutations. Again if mutations are involved you're only going to get something blurry or delay in the formation of a new species.

What you are calling new "species" is really just varieties or breeds of existing species, presumably having reached a point where they no longer interbreed with their mother populations, probably due to severe genetic depletion in some cases. And breeders could very well create a new species by that artificial definition if they keep at a particular breeding line without introducing new genes from time to time.

With respect to the creation of new species it is stasis, it is not evolution. With mutations you are getting traits showing up in individuals here and there in a population that is not changing overall. That's stasis.

If the only way to get a ceramic pot out of a hunk of clay is to pare away all the stuff that doesn't look like the ceramic pot, you aren't going to get the ceramic pot if you carve a little then add a little clay somewhere else and so on. Carve and add carve and add, no, that is not how it works in reality.

What you guys seem not to appreciate is that the existing alleles and genes in a genetically diverse population are more than sufficient to form many many subspecies through selection and isolation of portions of the gene pool. New gene frequencies are all it takes, new combinations of old alleles. All the breeds of dogs came about from nothing more than this, also the cattle breeds, the cats, etc. etc. The alleles in the original wild populations are merely potential or latent, the traits they govern hidden from view as it were but when selected in new combinations they produce an amazing array of new traits and phenotypes. You do not NEED mutations to get all the variety in living things we see. Which is a different argument from whether mutations occur and contribute. In my system mutations are simply not needed, and can interfere.

By which you mean what? That some individuals die off? Selection isn't occurring in any sense that produces a new species if there isn't reproductive isolation of what is being selected. Selection means particular traits are favored and multiply down the generations for that reason. That's the ONLY way you are going to get new traits in new combinations in an entire subpopulation. i.e. a new "species."

NOT UNLESS THERE IS SELECTION. Genetic drift is a form of selection so that new subpopulations can form within larger existing populations, that's one way but it's slow. But the entire population isn't going to evolve because a motley collection of new traits isn't evolution. Some of them have to be selected in order to get evolution.

I'm glad this is coming out now because it is SUCH a mistake. The same alleles and genes in NEW COMBINATIONS is all you need to form myriads of new varieties from a large genetically diverse population. The new combinations are brought about by the change in gene frequencies brought about by the reproductive isolation of a reduced number of individuals, making for a new gene pool of interbreeding individuals, and that's how new breeds, varieties, species come about. The new combinations are powerful sources of new traits. You do not need mutations.

The creation of novel traits occurs from new gene frequencies, new combinations of existing alleles.

You must be using the term "selection" in some other sense than I am. Selection is something that happens at the population level as I am using it. If perhaps you are talking about how sexual recombination works I guess that could be called selection with respect to individual traits, but I'm trying to keep the population level in mind which is where new species are formed.

Sounds plausible in the abstract but in reality it's not what happens, it does not describe what really occurs.

Message 187 of 1034 (692167) 02-28-2013 11:59 AM

Reply to: Message 185 by Faith 02-28-2013 11:00 AM

Perhaps you are misusing it.

Selection operates on the phenotypes of individuals. How could it be otherwise? It is individuals of a a population that compete with their fellows and with members of other species for food, safety, shelter, and of course mates.

Of course when looking at evolution, the plight of any single individual is of a minor consequence. When only one individual is involved, it might well be that despite being the only member with wings, that individual still gets eaten by an eagle. The consequences of selection is on populations.

Message 188 of 1034 (692168) 02-28-2013 12:04 PM

Reply to: Message 185 by Faith 02-28-2013 11:00 AM

In your system? Your system is about breeding and not evolution. Yes, mutations can interfere with breeding. But breeding does not produce new species.

This is just flat wrong. Genetic drift is the propagation of new traits in a population without selection.

Message 189 of 1034 (692173) 02-28-2013 12:50 PM

Reply to: Message 185 by Faith 02-28-2013 11:00 AM

In reality, species do change over time. We call it evolution.

Evolution is about speciation AND how traits appear in populations. It is both. Also, new traits also show up due to mutation. You are once again ignoring this fact. The black mice with the mc1r mutation are an example of this.

Before the reduction due to selection you get an increase in genetic diversity due to the accumulation of mutations. It is a sine wave, not an ever decreasing curve.

What we are calling species are genetically isolated gene pools. This causes different mutations to accumulate in each population, either through chance (neutral drift), or different selection pressures. What results is divergence. The two isolated populations become more diverse when compared to one another because they are accumulating different mutations.

What you fail to appreciate is that species who share a common ancestor are more divergent than can be produced by a single ancestral gene pool. The differences between human and chimp genes is not due to different alleles in our common ancestor. Those differences are due to lineage specific mutations.

Message 190 of 1034 (692175) 02-28-2013 1:16 PM

Reply to: Message 189 by Taq 02-28-2013 12:50 PM

Nice and succinct. These differences are the distinction between evolution and eugenics breeding programs which seems to be what Faith considers to be evolution.

Message 191 of 1034 (692177) 02-28-2013 1:31 PM

Reply to: Message 173 by Faith 02-28-2013 9:08 AM

quote:

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Well, would you agree that if the faucet and drain are both open you aren't getting evolution? That is, you aren't getting the development of new varieties/species/breeds?

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Definitely not.

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If you are getting more increase in diversity than you are selection events you also aren't getting evolution, the development of new varieties/species/breeds.

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Evolution isn't just the development of new species or subspecies. And anyway the increase in diversity is needed for the future development of new species and subspecies. (Your argument says so !)

quote:

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{ABE: As a matter of fact you can't have both faucet and drain operating at the same time. The "drain" is supposed to stand for the selection/isolation processes but those bring about new phenotypes FROM the genetic pool. Must be more like add THEN subtract, add THEN subtract in reality}

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That doesn't even make sense. The "faucet" is mutation and that is on all the time.

quote:

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What you are getting is perhaps new traits appearing here and there in individuals within the population. But for evolution to occur, that is the development of a new population with new characteristics, a new "species," you MUST have reproductive isolation/selection.

Doesn't that seem true to you?

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Well it seems poorly phrased. And it is far from clear that the usual model of speciation covers every case, It is certainly possible that some species come about from a more gradual transformation, affecting the entirety of the population,

quote:

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This analogy really doesn't work though because this isn't a simple addition/subtraction issue and I wish I had a model for what it really is. If mutation is involved it could maybe be described as something like two steps forward, one step back. Add some diversity, knock it back with selection, add some more diversity, knock it back again.

You HAVE to knock it back, that is, you HAVE to reduce the genetic diversity to get a new phenotype, breed, variety, species, in the wild as well as in domestic breeding, though the most accessible example is what happens in domestic breeding. If mutation really is involved it could only be a start-stop sort of thing along the lines I'm describing here, the continual adding of mutations merely delaying the inevitable.

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And here we come back to the idea of equilibrium. Now, let us grant that with the usual model of speciation the genes of the incipient species are less diverse than those of the parent population. It does not follow that they are less diverse than those of the parent population when it was an incipient species. This is the point you keep overlooking. The diversity of the parent population will have increased in the time between speciation events. Therefore there is no need for an inexorable reduction in genetic diversity.

quote:

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Mutations would keep changing the gene pool which sets back the selection effects, but it can't keep them from occurring IF you're going to get new "species." If all you get is balance or stasis, water in water out, again you aren't getting the production of new species, you aren't getting evolution.

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But of course you will because mutation does NOT act against selection in any way that would stop speciation. It does not prevent the loss of old alleles, it is NECESSARY to the rise of new alleles to replace the old. Your version of evolution is unworkable.

Message 193 of 1034 (692214) 03-01-2013 9:15 AM

Reply to: Message 185 by Faith 02-28-2013 11:00 AM

On the contrary, it's precisely what we see in reality. Almost every newly born organism possesses new mutations. The average human being possesses around 100 new mutations. Research has told us the mutation rate for many types of life, you can read about it over at the Wikipedia article on Mutation Rate.

Despite all these new mutations flowing into species population the world over, what you called "delineated recognizable species" continue to exist. That's because mutations, at least those that yield viable offspring, cause only tiny changes, and many are neutral.

Species are not eternal forms persisting forever. Species are plastic and change over time. As environments change species gradually change to adapt. Even when environments are constant species still change due to the genetic drift that is a result of the imperfect copying of reproduction that introduces new mutations.

It would be incorrect to say that this is only what we theorize might happen. It is precisely what we know happens because research has revealed it happening. We know that reproduction is almost always imperfect and causes mutations because there have been studies of life ranging from bacteria to mammals that reveal these mutations occurring. And we know the effects of mutations that create viable offspring are tiny. And we know that despite this species remain the same species over many, many generations. It probably takes at least 10,000 generations to produce a new species under normal circumstances.

Yes, you're right. In reality species boundaries can be blurry, as illustrated by ring species that blend into each other at the boundaries of their territories. And yes, species are constantly changing, too, though not on human timescales.

That species boundaries can be blurry is responsible for the species definition problem. While we have no problem telling that cats and dogs are different species, its much more difficult when determining whether wolves and dogs are different species, or whether gray squirrels and red squirrels are different species. Biologists use a variety of methods to determine whether two phenotypically very similar species are the actually same species, but the most common is genetic analysis.

Any breeding population of organisms is an identifiable species, regardless of the particular qualities of the species.

No, it's not theory, it's reality. There is nothing that can stop the imperfect copying of reproduction that results in mutations, and environments are constantly imposing selective pressures on populations. All species populations are always simultaneously experiencing both mutation and selection. There's is no possible way to prevent either from occurring.

Without mutation you cannot get a new species. You can, for example, select for domesticity in wolves and foxes and find that other traits, such as curled tails, emerge at the same time, but neither domesticity nor curled tails are new traits. Rather, they were already present in the parent population but to only a tiny degree, and breeding develops and emphasizes these traits. But dogs and tame foxes can still breed with the original wolves and foxes because they are still the same species. Isolation and selection alone does not create new species. If it did then breeders would be creating new species all the time.

Then why can't breeders create new species?

No, it should not happen that a new species emerges by "new mixes of old alleles". If a subpopulation has all the same genes and alleles of the original population then these populations can still interbreed and are still the same species.

Plus your approach will never yield what we actually see in nature, which is that only very, very similar species have the same genes. Any species whose differences are more than slight will have different genes and alleles. Your conception will never produce different genes between species, which is precisely what we see in nature.

What we should see in nature were your view correct is a species heredity chart like this where the parent population has all the genes and alleles of all the daughter and grand-daughter populations while the daughter populations have only subsets of the parent's genes and alleles. And the grand-daughter populations should have subsets of the daughter populations' genes and alleles:

                                            parent pop
                                                |
                         --------------------------------------------------
                         |                                                |
                   daughter pop 1                                  daughter pop 2
                         |                                                |
          -------------------------------                 -------------------------------
          |                             |                 |                             |
  daughter pop 1a               daughter pop 1b    daughter pop 2a               daughter pop 2b

What you need to find in order to have evidence that your scenario is something that actually happens is to find that every gene and allele in the daughter populations is already present in the parent population. And you need to find that every gene and allele in the granddaughter populations is already present in the daughter and parent populations.

But something like this has never been found, not in nature and not in breeding programs.

No, that's pretty much how it works in reality, except for the part about having the specific goal of a ceramic pot. Evolution has no specific goals, just the general goal of adaptation to the environment.

Of course we understand that one can form many subspecies from a single set of genes and alleles. But one cannot form a new species unless one has a supply of new genes and alleles.

I think you must be operating under the misimpression that main populations do not undergo selection. That would be incorrect. The processes of mutation and selection are always in operation in all populations everywhere.

This would be incorrect. A subpopulation with all the same genes and a subset of the alleles will still be the same species. It will still be able to interbreed with the main population. You cannot create a new species without new genes and alleles.

What I said is true of both individuals and populations. Let me say it again in terms that are specific to a population. Selection operates continuously upon all expressed portions of the gene pool of a population, including newly expressed portions due to mutation.

Again, we think this is what occurs in reality because when we looked at reality this is what we observed happening. We observed that almost all reproductive events include a small number of mutations. We observed that the environment is always exerting selection pressures on populations.

--Percy

Message 194 of 1034 (692234) 03-01-2013 10:50 AM

Reply to: Message 193 by Percy 03-01-2013 9:15 AM

Exactly. And alternatively if creating species is about stomping out diversity, how is it that border collies, Danes, poodles, Labs (of all colors, world's best non human companions), Chihuahuas, bulldogs, spaniels(all types), Terriers, Shih Tzus, and yes, those mutated dachshunds and countless others are all of the same species.

Or this: If you can have mutations and still be human, then eliminating or preventing such variation or diversity is not a part of forming a human species.

Seriously, is there really anything left of this "End of Evolution" stuff? Because absent some new argument, I think a mud hole has been stomped in 'Evolution Requires Reduction in Genetic Diversity'.

Message 195 of 1034 (692246) 03-01-2013 11:40 AM

Reply to: Message 168 by PaulK 02-28-2013 1:48 AM

According to my model on the other hand, I would say that the odds favor its having been latent in the gene pool and then brought to expression in a combination that's rare for that gene pool through mere sexual recombination. There are many ways a trait could be latent, starting with its allele(s) being rare in that particular collection of gene frequencies, but also including its not being expressed except as the product of particular alleles for a number of different genes in combination, prehaps also involving formerly unexpressed recessive alleles, or even dominant alleles that don't show up as visible traits except in particular combinations.

Yes I understand that the argument I'm facing here involves the claim that breeding methods don't model evolution in the wild, but it IS my argument that the principles are the same no matter who or what is doing the selecting.

Since it has been acknowledged by at least a few here that developing new breeds does involve reducing genetic diversity through mere selection of particular traits, and it's not an unreasonable idea that selection processes in the wild would operate in the same way, then the same kinds of processes would have to tend to the same conclusion, and they do, as exampled I believe in speciation events. Except of course in the wild the selection processes can be quite random such as migration and geographical isolation of a new gene pool which is not usually as small as those used in breeding, rather than caused by anything as actively selective as Natural Selection, though that may operate as well in some situations.

Seems to me we have Darwin himself for an authority on the similarity with domestic selection as he drew his inspiration for natural selection from his own experiences with breeding pigeons, and extrapolated his method to the random influences found in nature. He was able to produce quite an array of spectacular pigeon variations simply by selecting individuals to mate for chosen traits, and made the very reasonable observation that nature must do something similar in order to get the many variations we see there; such as the differences between mainland turtles and the turtles on the Galapagos, as well as all those different kinds of finches. He was right of course, he just went too far with it.

You all assume (without proof) that the traits chosen for breeding are created by mutation and there really isn't any way I can prove you wrong, but I don't see how you could claim that when the same trait is selected generation after generation with the effect that the chosen trait becomes strikingly large and elaborate, that mutations for each of those expansions and elaborations were the cause in each generation. Not if mutation is truly random you can't. The more reasonable explanation is that there is something in the genetic design itself that is capable of such elaborations.

IF you are really observing a mutation and not confusing it with a normally occurring latent allele. But what KIND of diversity is NOT known in all cases. What is best known is the mutations that cause genetic diseases.

Often deleterious ones.

Yes and no. You are all more or less willing to accept ANY kind of change as valid in supporting your position, including deleterious changes. That isn't impressive to someone who thinks evolution has to produce changes that can be useful to the organism, no matter how cleverly you rationalize the possibility of a disease process sort of becoming useful in various contexts. Which as far as what is actually known is concerned is a very rare occurrence and the only one I can think of at the moment is the fact that sickle cell anemia protects against malaria. Not a hopeful situation for evolution it seems to me but then who am I to have an opinion?

You aren't listing your evidence here but as I've encountered it most of the actual evidence that IS evidence is just as good evidence for creation as it is for evolution, often better, but besides that your evidence often amounts to wild interpretations, as of the fossil record, which creationists rightly laugh at. Or finding that since the octopus has an eye most similar to a human eye that proves that the human eye evolved even though there is no known genetic path, or even theoretical genetic path, that could have brought that about. And that sort of nonsense is treated as "evidence." Chortle.

Not an assumption, this is really and truly what I recognized had to be true as I was following out arguments on this subject. Certainly no assumption. It was a very exciting discovery as a matter of fact. But of course proving it is an uphill battle, especially with all the evolutionists trying to throw me over the cliff. Good thing I bounce well.

Edited by Faith, : No reason given.