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Christian Faith Requires the Acceptance of Creationism

shernren

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What, precisely, is a genetic bottleneck?

I think it is becoming clear to all that you are simply critiquing your own understanding of evolutionary theory, and that your own understanding of evolutionary theory is shallow if not outright wrong.
 
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gluadys

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The reproduction of individuals is the means by which genetic modifications are transmitted and spread in a population.

The reproduction of individuals is the means by which genetic modifications are spread to their descendants. But that doesn't make their descendants anything more than a variant group within the species. It doesn't account for change in the populations.

If you have in one generation 10 individuals born with a specific genetic change and each passes on that change to its descendants (and meanwhile 99% of the individuals are passing on their unchanged genes to their descendants) you get Mendelian balance, not an evolving population. You now have a population which is mostly in stasis (little to no physical change in form) with 10 different variants.

So reproduction alone does not account for evolution. You need a pattern of reproduction that allows one variant to become more common in the population. You need one of those individuals to have more descendants than others on a consistent (non-random) basis.




I was pointing out the fact that scientists do not stick with the biological definition in practice. It would be unreasonable to do so. There are many species that are capable of breeding with other species.

Ah, there's your error. The biological definition of species does not exclude the capacity of breeding with other species (as long as they are closely related). The biological definition of species (applicable only to sexual reproduction) is that the two species do not normally interbreed in nature. The key verb is "do" not "can". The occasional hybrid mating does not violate this definition. Nor does hybrid mating in non-natural conditions.

So scientists are sticking with the biological definition. You are using a narrower definition than scientists do.





In the taxonomic system,a genus is a group of species that are structurally similar,even if they have not been seen to be related.

That used to be true. It was the only definition possible under the Linnaean system which did not consider biological relationships.

However, what the theory of evolution does is explain why a group of species is structurally similar. They have similar structures because they inherited them from the same ancestor. So, the structural definition ties into the common descent definition in that common descent makes sense of the structural definition. And especially of the way structural similarities are distributed among species. (nested hierarchy). The only known process that naturally produces a nested hierarchy is descent from common ancestors.

The evolutionary explanation also allows us to predict less obvious features than structure as well. Species which inherit the same physical structure also inherit the genes which govern the production of those structures. So we should expect a genetic as well as a structural resemblance.

And we find that is the case.

Even though species in the same genus have similar structure, they also differ in unique ways. We should find genetic differences which correspond to those differences. And we do.

We can even do a sort of "genetic archeology" and find in species genes used by their ancestors that are not used today such as the genes for teeth in chickens or the GULO gene (which synthesizes vitamin C in most mammals) in humans and other hominids where it is non-functional.

The GULO gene is particularly interesting because hominids not only have a non-functional gene: it is non-functional for the same reason. There are a few other mammals that also have a non-functional GULO gene, but the reason for the lack of function is different.

One has to ask: what are the chances that structurally similar but non-related species would not only share a genetic defect, but the very same genetic defect, if they did not all inherit it from the same ancestor.





Phylogenetic research cannot show that there was ever reproductive relatedness between species.

That depends on what you accept as evidence. If you don't even accept the sort of DNA evidence used to establish paternity, then, of course, you have hamstrung phylogenetic research.





We cannot know if there was common descent between species unless they have been seen to be reproductively compatible or if one group has been seen to emerge from another.

We can only document common descent through observation when we can actually study the dividing of populations in real time. That's true. But we can infer the probability of common descent from evidence in cases where direct observation is not possible. This is a perfectly legitimate scientific procedure. It is the sort of science that a weather forecast is based on. That is why your weather reporter will tell you what the probability of precipitation is in your area over the next 24 hours. It is also the way DNA is used in cases of disputed paternity. The biochemist who analyzes the DNA samples will report not that so-and-so IS the father of the child, but that there is X% probability that he is. In exactly the same way, we can estimate the probability that two species have the same ancestor. And how remote in time (and generations) that ancestor is.



I said no because you did not describe macro-evolution. Your definition of genus was wrong anyway.

You are describing macro-evolution as a degree of change. But if you ignore the process of how the change happens, you are not really describing macro-evolution.

My definition was not incorrect. Above, you yourself spoke of a genus as composed of species that are structurally similar. Well, the two species we end up with after a speciation, are structurally similar. So they constitute a genus, even by your definition.



I know that it is not the process. I don't believe macro-evolution happened so I do not call it results either.


Whether you believe it happened or not, you still have an idea of what it is supposed to be. As I said "macro-evolution" can apply both to the description of resulting changes and to the process by which those changes happened. It would make sense to say you don't believe in macro-evolution if by that you meant that the process described cannot produce the observed differences. That is something we could discuss.

But a simple a priori disbelief in macro-evolution cannot be argued with because it has no rational foundation.




Speciation by definition results in species. The populations would have been sub-species prior to speciation, but now they are species. That is why Darwin called sub-species "incipient species". Yes, they do, at the time, have less genetic variability than the original population. However, there are other processes that increase the variability of any species--so this is not a permanent situation.

What is key to macro-evolution, is that since speciation has occurred, the increase in variability in the two species will not be the same. Nor will it be homogenized through interbreeding (as it can be so long as they are only sub-species). Nor will the moulding of the new variability in particular directions by natural selection be the same. So post-speciation, the species will inevitably diverge from one another. This sets the stage for those big differences that you identify as macro-evolution.

Macroevolution, the process produces macroevolution, the history of big changes. If you understand the process, the changes are not such a mystery.


Evolution is explained with reference to changes of allele frequencies,but that is not the proper definition. Evolution refers to changes in physical form,not statistical changes of DNA.

Again, they are tied together. A change in an allele produces a changed trait in an individual who passes that change on to its descendants. And if its descendants (through natural selection) are represented in greater proportion in the next generations, that allele changes frequency in the population. And that changes not just one or a few individuals, but the character of the species. And that is what evolution is: changes in the character of the species. (not all evolution is about physical form though. Biochemical, physiological and behavioral changes also count as evolution.)


I look at the supposed causes,as well as the supposed results. That is why I do not believe that macro-evolution happened. The supposed causes - natural selection and genetic mutation - cannot possibly lead to macro-evolution.

Those are the two principal causes, but not the only ones. Speciation is crucial to macro-evolution, though not to evolution within a species. So you need to re-examine your understanding of the causes.



Macro-evolution cannot be shown to have happened,and it does not logically or biologically follow that populations will develop beyond the species level because of genetic isolation. It just does not happen that way.


Speciation has been shown to have happened. And speciation, by definition, produces groups that are above the species level.




It is wrong to extrapolate macro-evolution from the observed instances of speciation.

There is no extrapolation involved. Observed instances of speciation are observed instances of macro-evolution. By definition, they add new species to a genus--expanding the boundaries of a genus.

I know you want to see how the higher taxa, families, orders, etc arise. But no new special process is needed. If you already have 3 species in genus, and each of them divide into new species, then you now have three groups of two species each. What designation will you give to each of these groups?

If you decide to call each of these three groups a genus, then what do you call the group of six species--which now contains three genera?
 
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mark kennedy

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I have looked into this several times and where this leads is to Chromosome 8. While I don't have time for direct comparisons of the GULO there are direct comparisons of Chromosome 8 that make some counter-intuitive observations:

Molecular genetics and developmental studies have identified 21 genes in this region (ADRA1A, ARHGEF10, CHRNA2, CHRNA6, CHRNB3, DKK4, DPYSL2, EGR3, FGF17, FGF20, FGFR1, FZD3, LDL, NAT2, NEF3, NRG1, PCM1, PLAT, PPP3CC, SFRP1 and VMAT1/SLC18A1) that are most likely to contribute to neuropsychiatric disorders (schizophrenia, autism, bipolar disorder and depression), neurodegenerative disorders (Parkinson's and Alzheimer's disease) and cancer. Furthermore, at least seven nonprotein-coding RNAs (microRNAs) are located at 8p. Molecular Psychiatry 14, 563-589 (June 2009)

That raises some red flags for me, hard to imagine that selective pressure is going to allow a lot of divergence during the evolutionary process from chimpanzee/human common ancestry.

Region Displayed: 0-146M bp
Total Genes On Chromosome: 1317
NCBI Genome Map Viewer, Chromosome 8

Region Displayed: 0-144M bp
Total Genes On Chromosome: 1097
NCBI Genome Map Viewer, Chromosome 8

What these homology arguments never do is to take into consideration the inverse logic. If things in common are evidence for common ancestry then are differences a valid argument against?

Chromosome 8 in humans and chimpanzees diverge by about 2 million base pairs and over 2,000 genes according to these two maps. Perhaps there is an explanation I'm not aware of but if we are talking about direct comparisons of a single defunct gene perhaps the search should be expanded to include highly conserved genes involved in the development of the human brain from that of apes.

Grace and peace,
Mark
 
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shernren

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That raises some red flags for me, hard to imagine that selective pressure is going to allow a lot of divergence during the evolutionary process from chimpanzee/human common ancestry.

Can you explain what you mean in simple English or are you just parroting some terms you heard sfs once use before?

(Were it the former, you would know that most of the time it is selective pressure that causes divergence, before preserving it.)
 
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gluadys

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That raises some red flags for me, hard to imagine that selective pressure is going to allow a lot of divergence during the evolutionary process from chimpanzee/human common ancestry.

Why is that hard for you to imagine?



What these homology arguments never do is to take into consideration the inverse logic. If things in common are evidence for common ancestry then are differences a valid argument against?

Yes, of course. Differences can be due to evolutionary changes since the lineages diverged from their last common ancestor. I expect most differences between chimpanzees and humans would fall into this class.

Or differences can be due to species having different recent ancestry but also have similarities due either to a more remote common ancestry or to convergent evolution.




I am sure it has been.


In any case, none of this is relevant to the GULO pseudogene in hominids or offers any meaningful alternative to common ancestry.
 
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Anthony Puccetti

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What, precisely, is a genetic bottleneck?

A decline in genetic variation in a population that has sharply decreased in numbers.

I think it is becoming clear to all that you are simply critiquing your own understanding of evolutionary theory, and that your own understanding of evolutionary theory is shallow if not outright wrong.

I critique what scientists and theistic evolutionists say about the theory.
 
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Anthony Puccetti

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A variant group within a species is change in a population. Not change above the species level,but still change. Variance is change.


It depends upon the size of the population and the extent to which the descendants reproduce generation after generation. 10 individuals with variant genes can beget a hundred descendants,which in turn can beget a thousand. It isn't like there is a specific dividing line between a population in stasis and a population that is changing.


What you described still boils down to reproduction being the means of change in a species. When I said that change in a species is due to reproduction,I was not suggesting that a whole species could be changed with a single generation of a few individuals. I was talking about the phenomenon of reproduction,both as an individual event and as collective events that happen over many generations. Whole populations exist as individuals that are reproduced and reproduce,so when variants become more common in a population it is ultimately due to reproduction.
 
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Anthony Puccetti

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Good. Now, does speciation cause bottlenecks?

Continued instances of speciation can lead to a bottleneck if there is a sharp decrease in the size of a population.
A genetic bottleneck,and not macro-evolution,is the farthest extent of what follows from accumulated mutations and continued branching and speciations.
 
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gluadys

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A variant group within a species is change in a population. Not change above the species level,but still change. Variance is change.

Ah, but I did not speak of a variant group. The first instance of a variation necessarily occurs in an individual. How do we get from that to an identifiable variant group?

Note that two things have to happen.

1. The variation must be passed on to others in the population, but
2. it must be passed on preferentially to some and not others.

If it passed randomly through a population, there would be many individuals with that trait, but no variant group. (This is more or less the case with red hair--there is no one group of humans identified by red hair; but many groups of humans include some individuals with red hair.)




When I said "the other 99%" I implied that these 10 were one percent of the population. That means there are 990 others. Yes, these ten can beget a hundred descendants and those in turn a thousand. But the 990 can beget 9900 descendants and those in turn 99000. And what this means is that the variant genes now inherited by 1000 descendants are right where they were two generations back: at one percent in a population of 100,000.

This is not changing the population; this is not evolution.



Whole populations exist as individuals that are reproduced and reproduce,so when variants become more common in a population it is ultimately due to reproduction.

But as you see above, (and as Mendel discovered) reproduction alone does not make variants more common. So how do they become more common?
 
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Anthony Puccetti

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Ah, but I did not speak of a variant group.

You did. See post 322.

The first instance of a variation necessarily occurs in an individual. How do we get from that to an identifiable variant group?
Variant individuals multiply through reproduction,and may become separated and reproductively isolated from the group they sprang from.
Note that two things have to happen.

1. The variation must be passed on to others in the population, but
2. it must be passed on preferentially to some and not others.
The "selective" process is secondary to reproduction,and it boils down to individual acts of reproduction.

The pigmentation of hair is not enough to make a different species anyway.

Evolution is not always about a population changing on the whole,it is often about one population branching and diverging from another. So if a large variant group of South American fruit flies is discovered in a different region from the group it sprang from,what is to prevent scientists from giving it a new species name?

But as you see above, (and as Mendel discovered) reproduction alone does not make variants more common. So how do they become more common?
The PROPORTION of variants increases as the numbers of the original group decreases through natural elimination (i.e. natural selection). But evolution is not always about an increase in proportion of variants or allele frequency. Evolution often refers to the BRANCHING of new species from prior ones,not to the transformation of species. The new variant group does not have to become the majority in the group it originated from to be called a new species. It can just be branched from the original group.

Reproduction may not be the only reason why variants become more common,but it is the reason they emerge from prior species in the first place,and why they increase in numbers.
 
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gluadys

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Now, and especially toward the end of this post, you are making some very good points. You are now demonstrating that when pushed to it, you can describe the evolutionary process very accurately. Thank you.

Yes, the difference between variant individuals scattered in a population (like people with freckles) and an identifiable variant group (like certain breeds of dogs) is that the group is at least partially isolated from the group they sprang from. Breeders enforce that isolation artificially, mating like with like and not allowing hybrid crosses. In nature there are various causes of group isolation that reduce contact between populations and an isolated group can develop variant characteristics that stay in the group, making it a distinct variety or sub-species. This is an important step toward speciation.

You still haven't fully expressed though, how a variation which is first expressed in an individual manages to become distributed through even this isolated group. (But I see that you get to that later.)


The pigmentation of hair is not enough to make a different species anyway.

That's ok. At this point our focus is on variant individuals and variant groups within a species--not a new species yet.


They would need to check on whether it is reproductively isolated as well as geographically isolated from the ancestral group. If they take some individuals from both groups and put them in mixed quarters, will they mate at random or will each group prefer mates from its own group? (Assortative mating). If they mate at random such that over a few generations the two groups fuse, they would call the two groups in their natural setting geographical subspecies of one species. If they do not mate at random, they might call them species, but maybe still sub-species. If hybid matings produce non-viable or sterile offspring or offspring that do not thrive as well as those whose parents are both from the same group, then they would certainly call the new group a new species.

Of course, scientists might indeed call the newly discovered group a new species when it is first discovered, but for that to stick they would have to convince other scientists that it is a new species through various tests before the new name would be officially registered by the international taxonomic authorities. There are plenty of instances when the discoverer of a new group has said "Look! a new species" and further research has shown that it is actually a form of a species already registered. So there are criteria that have to be met before the scientific community will take the word of a first discoverer that he/she has really found a new species.

The PROPORTION of variants increases as the numbers of the original group decreases through natural elimination (i.e. natural selection).


There we have it! Now you have just defined evolution scientifically and correctly named the cause. Natural selection is the key mechanism that takes a variant from one or a few scattered individuals in a population to most of the population. If the species is to change, there has to be either a higher rate of mortality among those without the variant character or a greater rate of reproduction among those with the variant character. (And some would consider those synonymous--just different ways of saying the same thing.) This not only spreads the variant among the descendants of the first individual to express it, but assures that his descendants will progressively become a larger and larger proportion of the population.

That is how the change becomes a species change. That is evolution.





Correct again. You have just described cladistic (i.e. branching) speciation. You have just described macroevolution. This is how most macroevolution happens. Your example of a new species of South American fruit fly was also an example of cladistic speciation. And that makes it an example of macroevolution. One species emerging from another because something happened to separate their ancestors from the larger ancestral group and their evolution moved along a different path than that of the group their ancestors separated from.

Reproduction may not be the only reason why variants become more common,but reproduction is the reason they emerge from prior species in the first place,and why they increase in numbers.

True, everything begins with reproduction. But as noted above, it isn't just increase in numbers that is important, but increase in the proportion of the population. After all, both those with and those without a new variant character will continue to reproduce. So species change only happens when one group reproduces more successfully than the other--increasing the number of its descendants more rapidly than the other.

And one of the most common ways for that to happen is not by changing the whole species but by isolating a small group which is subjected to different selective factors which over time results in cladistic speciation.


Anthony, I want to thank you, very sincerely.

In the past I have pushed others the same way I have pushed you; and most of the time, people refuse to think things through. They get so fixated on the origin of variation that they identify that alone as evolution without considering how a variation moves into a species and changes a species.

You persevered. And it is clear we have ended up in an agreement of how evolution happens with assignment of key functions to variation, reproduction, natural selection and cladistic speciation.

This is how evolution happens. This is how macroevolution happens.
 
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