We are no longer 99% similar to chimps

[mark kennedy]

And they not only represent 3x more divergence between humans and chimps, but within sea urchins, thale cress, fruit flies, nematodes, and E. coli. In other words, once ways to closely investigate indels were developed, indels were found to make up a lot more mutational changes in base pairs than single-base substitutions - across the whole tree of life, not just in our own peculiar branch. Your mistake is to act as if it is something particular to human-chimp divergence. It isn't, everywhere there is DNA you see indels contributing a lot of change.

So you have comparisions of sea urchins, thale cress, fruit flies and hopefully mammals to back that up right?

Want to explain why the evolution we see in HARs is physically impossible and get your Nobel? Hint: a physical argument of impossibility would be helpful here, not just some hasty probability calculations and your say-so that it doesn't make sense.

Oh brother, you really don't look very closely at this do you? First take a quick look at this.

http://www.docpollard.com/HARs.html

Then consider this:

In order to investigate substitution rates in individual lineages, we computed the posterior expected number of substitutions on each branch of the 17 species tree using the method described in Siepel et al. [38]. The normalized human substitution rate exceeds the rate in the chimp-rodent phylogeny in all of the HARs, as expected. In HAR1–HAR5, the average estimated human substitution rate per site per million y is 26 times higher than the chimp-mouse rate (Table S5). Directly comparing substitution rates per site in the human and chimp branches (over the same period of evolutionary time), the human rate is an average of seven times higher than the chimp rate in HAR1–HAR5 (Table S5) and exceeds the chimp rate by more than 30% in all but three (1.5%) of the 202 HARs​

Forces Shaping the Fastest Evolving Regions in the Human Genome, PLoS available online)

I used to have trouble finding this sort of thing and now I can't get to all of it.

This is 100% consistent with the Creationist position that the fossils are either ape or human. No one is suggesting that neither the apes nor humans have not or do not evolve, their alleles do change over time. It just seems odd that every fossil dug up in Africa is immediately identified as one of our ancestors. Some look more like chimpanzee and gorilla ancestors but that possibility is never explored apart from being a common ancestor. It's an a priori assumption that is distorting our understanding of the fossil record.

You've got to be kidding. I brought this up the last time you made this erroneous claim and you didn't address it:

Why would I be kidding, lets see what you've got:

Early humans, on the other hand, lived in areas more arid areas conducive to fossil preservation but relatively hostile to chimp survival, such as the East Africa Rift Valley. “It’s the last place you’d expect to find chimps,” says anthropologist Jay Kelley of the University of Illinois at Chicago, US.But in a sediment of the Kapthurin Formation in the Eastern Rift Valley, Sally McBrearty of the University of Connecticut and Nina Jablonski of the California Academy of Sciences did find three fossils with the unambiguous characteristics of chimp teeth.​

First convincing chimp fossil discovered, 31 August 2005

Notice the title and the date, by the way, this was announced in the same issue of Nature the the Chimpanzee Genome sequence. Seems a bit odd that after 150 years they finally come up with a chimpanzee fossil, let's see what they uncovered:

"The two incisors and a molar, probably all from the same individual, date from around 500,000 years ago. They were found in sediments that include fossils of two early humans - Homo erectus or Homo rhodensiensis"

Two incisors and a molar...WOW! Exactly how many human ancestor specimans would you say they have uncovered?

No, we've been facing up to the indels and showing that this indel thing isn't unique to humans as you insinuate, in fact it happens all across the tree of life. The entire reason we didn't have a good rate for indels is because indels were difficult to study before this. But now we roughly know that indels happen roughly 1/10 as often as single-base substitutions and guess what, the indels we see in chimp-human divergence are right up this alley.

Still waiting for you to support that assertion.

I was responding quite specifically to busterdog's question of why mere similarity was being emphasized, and also to your quotemines of Darwin, as well as the same oversimplifications that you've been pushing elsewhere. I have too much time on my hands, live with it.

First of all I didn't quote Darwin, you did. I was trying to make things more comprehensive for him since he couldn't make heads or tails of my previous posts. Then you bust in being confrontational for what reason I have yet to figure out.

Coding segments: 99.4% similarity. There's a statistic that hasn't changed throughout this hustle.

Try looking at the direct comparisons and we can talk some more about that.

As for GULOP, not only do all the copies of the genes harbor the exact same deletion at the exact same site, but all-but-two of the single-base substitutions also follow phylogeny (whatever phylogeny you can construct from a single gene fragment over merely four species). The discussion is here: http://www.christianforums.com/t4109582&page=2[/quote]

Why don't you check this out and we can do a direct comparison:

UCSC Genome Browser on Chimp Mar 2006 Assembly

Please cite for "currently estimated to be close to the point mutation rate" - as far as the sources we've seen go, it's more like one-tenth the point mutation rate.

I did, I quoted sfs and linked to the thread. I'll dig it up again if need be but I don't think you want me to do that.

Mere semantics. If indels are a major source of gene defects, that does not preclude indels also being a major source of adaptive changes in genes as well. It's a little like saying the Middle East is a major source of terrorism - that doesn't disprove that the Middle East is also a major source of oil.

A major source of genetic defects is mere semantics?

I simply don't get how you read "natural selection was not much of an explanation for the neural system" out of this. He clearly stated how natural selection could act to form the eye and exactly what we would expect to see in living organisms today as a result. That's miles away from what you're trying to make him say.

Even the Chimpanzee Genome Consortium said that natural selection was not a factor. They attributed it to regional variations in the mutation rate. Now it is becoming apparent (check the paper I quoted, cited and linked) that even that doesn not explain it.

Not argument from credulity, argument from evidence.

You even dismiss Sir Fancis Bacon, tsk tsk.

 

[shernren]

You know what mark, I hate to resort to ad hominems, but these arguments:

As for GULOP, not only do all the copies of the genes harbor the exact same deletion at the exact same site, but all-but-two of the single-base substitutions also follow phylogeny (whatever phylogeny you can construct from a single gene fragment over merely four species). The discussion is here: http://www.christianforums.com/t4109582&page=2

Why don't you check this out and we can do a direct comparison:

UCSC Genome Browser on Chimp Mar 2006 Assembly

Even the Chimpanzee Genome Consortium said that natural selection was not a factor. They attributed it to regional variations in the mutation rate. Now it is becoming apparent (check the paper I quoted, cited and linked) that even that doesn not explain it.

have been thoroughly discussed to death, and yet you resurrect them like none of us here exist to tell you you're wrong. In the case of GULOP, the link I provided does give precisely a base-by-base comparison of the rat, macaque, orangutan, chimpanzee, and human GULOP gene, with discussion of how the mutations fall in step with a phylogenetic tree. In the case of "natural selection was not a factor", we discussed it here:

http://www.christianforums.com/showpost.php?p=28896255&postcount=145
http://www.christianforums.com/showpost.php?p=28928142&postcount=154

What is being explained here? It's not human-chimp divergence per se, it's large-scale variation between human-chimp divergence rates. When a simple model is used where divergence rates between different sites of human-chimp comparisons are identical, the predicted standard deviation of the divergences are 0.02%. In reality, however, the standard deviation comes up to about 0.25% ie divergence is far more variable than expected.

This does not mean "I can't believe it's not human!" - not that overall divergence is far higher than evolution can explain. It means that some areas diverge less and some areas more than a simple model would predict, hence causing a very large range of divergences observed.

...

If chimp-human divergence is more variable than a simple model predicts, does this mean that it is higher overall than a simple model predicts?

And for bonus marks, just what does the word "regional" in the above article mean? What "regions" are being referred to here?
​

The fact that you are using arguments that have long been refuted, or at least have strenuous objections against them that have not been answered, speaks volumes about your exemplary objectivity and respect for truth.

So you have comparisons of sea urchins, thale cress, fruit flies and hopefully mammals to back that up right?

Chimps and humans are mammals, aren't they? I've provided data that shows that life can undergo this amount of indel variation (and not speciate, while we're at it), why don't you supply your statistics that show that mammals cannot?

Oh brother, you really don't look very closely at this do you? First take a quick look at this.

http://www.docpollard.com/HARs.html

Then consider this:

In order to investigate substitution rates in individual lineages, we computed the posterior expected number of substitutions on each branch of the 17 species tree using the method described in Siepel et al. [38]. The normalized human substitution rate exceeds the rate in the chimp-rodent phylogeny in all of the HARs, as expected. In HAR1–HAR5, the average estimated human substitution rate per site per million y is 26 times higher than the chimp-mouse rate (Table S5). Directly comparing substitution rates per site in the human and chimp branches (over the same period of evolutionary time), the human rate is an average of seven times higher than the chimp rate in HAR1–HAR5 (Table S5) and exceeds the chimp rate by more than 30% in all but three (1.5%) of the 202 HARs​

Forces Shaping the Fastest Evolving Regions in the Human Genome, PLoS available online)

I used to have trouble finding this sort of thing and now I can't get to all of it.

Actually, practically all the papers I've read are papers dredged up by you. I owe you that much. My main motivation for reading scientific papers is actually an innate curiosity to understand just how papers which blatantly outline plausible evolutionary mechanisms gets interpreted by you as "evolution can't explain them!", like this:

The accelerated elements, and in particular the top five, show a strong bias for AT to GC nucleotide changes and are disproportionately located in high recombination and high G+C content environments near telomeres, suggesting either biased gene conversion or isochore selection. In addition, the ratio of human polymorphism to human-chimp divergence is significantly lower around two of these elements than it is in the surrounding 1Mb, a finding which is consistent with a selective sweep. A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome.
​

http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020168.eor
(emphases added)

Now if you would just care to demonstrate how biased gene conversions, isochore selection, and selective sweeps are physically impossible, there's a Nobel waiting for you.

Why would I be kidding, lets see what you've got:

Early humans, on the other hand, lived in areas more arid areas conducive to fossil preservation but relatively hostile to chimp survival, such as the East Africa Rift Valley. “It’s the last place you’d expect to find chimps,” says anthropologist Jay Kelley of the University of Illinois at Chicago, US.But in a sediment of the Kapthurin Formation in the Eastern Rift Valley, Sally McBrearty of the University of Connecticut and Nina Jablonski of the California Academy of Sciences did find three fossils with the unambiguous characteristics of chimp teeth.​

First convincing chimp fossil discovered, 31 August 2005

Notice the title and the date, by the way, this was announced in the same issue of Nature the the Chimpanzee Genome sequence. Seems a bit odd that after 150 years they finally come up with a chimpanzee fossil, let's see what they uncovered:

"The two incisors and a molar, probably all from the same individual, date from around 500,000 years ago. They were found in sediments that include fossils of two early humans - Homo erectus or Homo rhodensiensis"

Two incisors and a molar...WOW! Exactly how many human ancestor specimans would you say they have uncovered?

It's not our fault chimp ancestors decided to live in regions with acidic soils. Why don't you bring up a specific specimen you think should represent a chimpanzee ancestor instead of a human ancestor and then we'll see. If you can't think of any such specific specimen, then you're admitting that the hominids we have right now couldn't possibly be mistaken for chimpanzee ancestors, and thus your argument is moot.

Still waiting for you to support that assertion.

I think I've cited that indel paper here at least ten times already:

Scientists see indels contribute 4-5 times, and even more, nucleotide variation than single-base substitutions routinely, across the phylogenetic tree. There is nothing amazing about seeing indels "dwarf" single-base substitutions by 4-5 times. It happens with other organisms and yet you never raise any complaints about those:

It was recently shown that indels are responsible for more than twice as many unmatched nucleotides as are base substitutions between samples of chimpanzee and human DNA. A larger sample has now been examined and the result is similar. The number of indels is

1/12th of the number of base substitutions and the average length of the indels is 36 nt, including indels up to 10 kb. The ratio (Ru) of unpaired nucleotides attributable to indels to those attributable to substitutions is 3.0 for this 2 million-nt chimp DNA sample compared with human. There is similar evidence of a large value of Ru for sea urchins from the polymorphism of a sample of Strongylocentrotus purpuratus DNA (Ru = 3-4). Other work indicates that similarly, per nucleotide affected, large differences are seen for indels in the DNA polymorphism of the plant Arabidopsis thaliana (Ru = 51). For the insect Drosophila melanogaster a high value of Ru (4.5) has been determined. For the nematode Caenorhabditis elegans the polymorphism data are incomplete but high values of Ru are likely. Comparison of two strains of Escherichia coli O157:H7 shows a preponderance of indels. Because these six examples are from very distant systematic groups the implication is that in general, for alignments of closely related DNA, indels are responsible for many more unmatched nucleotides than are base substitutions. Human genetic evidence suggests that indels are a major source of gene defects, indicating that indels are a significant source of evolutionary change.
​

http://www.pnas.org/cgi/content/full...urcetype=HWCIT

First of all I didn't quote Darwin, you did. I was trying to make things more comprehensive for him since he couldn't make heads or tails of my previous posts. Then you bust in being confrontational for what reason I have yet to figure out.

You're right that I was confrontational first. But oh well. You did refer to Darwin: Darwin admitted that the gradual development of the eye seemed unlikely in the extreme. When it came to the brain he just said the smallest human brain is about the same size of the largest ape brain. We now know that brains are built by highly specific and conserved genes that do not respond well to mutations. and your first sentence was a clear quotemine. He was being rhetorical as much as he was foreseeing difficulties.

A major source of genetic defects is mere semantics?

How d'you like being dismissed as being merely semantical? Fact is that if indels can cause genetic defects, indels can also undo genetic defects. If a deletion of AG can cause a defect, then an insertion of AG can undo that defect. And the undoing of a defect from a wild-type is a beneficial mutation. For example:

Another example is the dramatic increase in the size of human brains compared with the brains of their ape cousins, according to Dr. Christopher A. Walsh, chief of genetics at Children's Hospital Boston. He helped identify a gene that, when mutated, causes children to be born with brains less than half the normal size -- comparable, in fact, to the size of a chimpanzee brain. What is remarkable about the disease, called microcephaly, is that it is not deadly. It is debilitating, but patients can learn to walk on their own and sometimes even speak a few words.



It seems likely, Walsh suggested, that changes in this one gene, long ago, may have helped humans develop larger brains. The gene does not appear to be involved in regulating other genes, but it shows how a relatively small change can have a dramatic effect.
​

http://www.boston.com/news/science/...ging_the_way_we_think_about_evolution/?page=3

A mutation in a human gene reproduces effects of the wild-type chimp gene, and so is a source of genetic defect; but this mutation is merely undoing the original mutation which changed the wild-type chimp gene into the human gene, which was a beneficial mutation.

You even dismiss Sir Fancis Bacon, tsk tsk.

The last time I checked, argument from authority was also fallacious.

 

[mark kennedy]

have been thoroughly discussed to death, and yet you resurrect them like none of us here exist to tell you you're wrong. In the case of GULOP, the link I provided does give precisely a base-by-base comparison of the rat, macaque, orangutan, chimpanzee, and human GULOP gene, with discussion of how the mutations fall in step with a phylogenetic tree. In the case of "natural selection was not a factor", we discussed it here:

http://www.christianforums.com/showpost.php?p=28896255&postcount=145
http://www.christianforums.com/showpost.php?p=28928142&postcount=154

​

Obviously, I don't trust you sources and simply don't have the time or the inclination to track it down. I really don't care about psuedogenes and that is all I have to say about that.

What is being explained here? It's not human-chimp divergence per se, it's large-scale variation between human-chimp divergence rates. When a simple model is used where divergence rates between different sites of human-chimp comparisons are identical, the predicted standard deviation of the divergences are 0.02%. In reality, however, the standard deviation comes up to about 0.25% ie divergence is far more variable than expected.

This does not mean "I can't believe it's not human!" - not that overall divergence is far higher than evolution can explain. It means that some areas diverge less and some areas more than a simple model would predict, hence causing a very large range of divergences observed.

Simple explanations have been exhausted and apparently there is a scramble to explain divergence. Personally I have every confidence in that ability of main stream science to rationalize it away. You don't seem to realize that Creationists are aware of this research and understand why it's important.

...

If chimp-human divergence is more variable than a simple model predicts, does this mean that it is higher overall than a simple model predicts?

There are not a lot of choices here, natural selection, mutiregional variation, relaxed fucntional constraint. None of the explanations are definitive. The simple mantra of natural selection is useless, you would need an extraordinary number of mutations in neural genes. This alone causes unsolvable problems for the ape to human scenerio. Rationalize it away if you will and I really don't mind. I'm finding more detailed expositions of the divergance everytime I look into this. You don't seem to appreciate the persuasive authority at work here and it comes down to what you trust. Sure science can provide a lot of utilitarian resources but it is worse then worthless when it comes to primordial and prehistoric events that only happened in human imagination.

And for bonus marks, just what does the word "regional" in the above article mean? What "regions" are being referred to here?

It's the sequence in question, I'm not going into details because I'm a little strapped for time lately. We can get into this later but where a mutation happens can have a lot to do with whether or not it is fixed.

The fact that you are using arguments that have long been refuted, or at least have strenuous objections against them that have not been answered, speaks volumes about your exemplary objectivity and respect for truth.

Right, this incessant fault finding is a constant attack. Generally it focuses on semantical points and it's just another ad hominem fallacy. I'm not worried about that, evolutionists were doing their victory dance before I took an interest in genomics and will long after I'm through with it.

Chimps and humans are mammals, aren't they? I've provided data that shows that life can undergo this amount of indel variation (and not speciate, while we're at it), why don't you supply your statistics that show that mammals cannot?

For one thing you want to dwell on homology arguments about psuedogenes and don't seem to care about neural genes. Like I have been trying to point out to you and every evolutionists I have encountered in the past year the adaptation of the human brain from a apes is the prize.

Actually, practically all the papers I've read are papers dredged up by you. I owe you that much. My main motivation for reading scientific papers is actually an innate curiosity to understand just how papers which blatantly outline plausible evolutionary mechanisms gets interpreted by you as "evolution can't explain them!", like this:

The accelerated elements, and in particular the top five, show a strong bias for AT to GC nucleotide changes and are disproportionately located in high recombination and high G+C content environments near telomeres, suggesting either biased gene conversion or isochore selection. In addition, the ratio of human polymorphism to human-chimp divergence is significantly lower around two of these elements than it is in the surrounding 1Mb, a finding which is consistent with a selective sweep. A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome.
​

http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020168.eor
(emphases added)

Since there is no one explanation they have adopted this mutimutational blanket explanation. Mutations are not an evolutionary force as far as I can tell. The problem is that they must be the explanation or you are left with God creating creatures fully formed. Natural selection cherry picking random mutations doesn't work, multiregional varitations in mutation rates has been explored, now multimutational explanations. Mutations are explaining nothing by an attempt to make them explain everything. At the same time certain immune systems do accumulate random mutatoins with beneficial effects. It's not like they can't discern between deleterious and beneficial effects. The problem is there is no way of measuring beneficial effects since they are so rare.

Now if you would just care to demonstrate how biased gene conversions, isochore selection, and selective sweeps are physically impossible, there's a Nobel waiting for you.

I never said they can't happen and I know that they do. My contention is that for them to happen on the scale required for humans to evolve from apes is not only impossible it has all the markings of a modern myth.

It's not our fault chimp ancestors decided to live in regions with acidic soils. Why don't you bring up a specific specimen you think should represent a chimpanzee ancestor instead of a human ancestor and then we'll see. If you can't think of any such specific specimen, then you're admitting that the hominids we have right now couldn't possibly be mistaken for chimpanzee ancestors, and thus your argument is moot.

Standard rethoric, just offer a simple rationalization and dismiss the argument. The problem is that everytime an ape fossil is found in Africa it is immediatly declared a human ancestor. Only fossils dated over 4 mya can be consider common ancestors and a lot of that is a stretch. The Homo habilis specimans are probably prehistoric chimps. Their cranial capacity is consistant with a gradual decline in overall size. They were at one time bipedal from what I gather at least in a limited way. They did not evolve into humans they devolved into modern chimps and bonobos. There are also gorilla ancestors in the mix and some of the Asian samples are probably orangs.

I think I've cited that indel paper here at least ten times already:

Whatever.

Scientists see indels contribute 4-5 times, and even more, nucleotide variation than single-base substitutions routinely, across the phylogenetic tree. There is nothing amazing about seeing indels "dwarf" single-base substitutions by 4-5 times. It happens with other organisms and yet you never raise any complaints about those:

It was recently shown that indels are responsible for more than twice as many unmatched nucleotides as are base substitutions between samples of chimpanzee and human DNA. A larger sample has now been examined and the result is similar. The number of indels is

1/12th of the number of base substitutions and the average length of the indels is 36 nt, including indels up to 10 kb. The ratio (Ru) of unpaired nucleotides attributable to indels to those attributable to substitutions is 3.0 for this 2 million-nt chimp DNA sample compared with human. There is similar evidence of a large value of Ru for sea urchins from the polymorphism of a sample of Strongylocentrotus purpuratus DNA (Ru = 3-4). Other work indicates that similarly, per nucleotide affected, large differences are seen for indels in the DNA polymorphism of the plant Arabidopsis thaliana (Ru = 51). For the insect Drosophila melanogaster a high value of Ru (4.5) has been determined. For the nematode Caenorhabditis elegans the polymorphism data are incomplete but high values of Ru are likely. Comparison of two strains of Escherichia coli O157:H7 shows a preponderance of indels. Because these six examples are from very distant systematic groups the implication is that in general, for alignments of closely related DNA, indels are responsible for many more unmatched nucleotides than are base substitutions. Human genetic evidence suggests that indels are a major source of gene defects, indicating that indels are a significant source of evolutionary change.
​

http://www.pnas.org/cgi/content/full...urcetype=HWCIT

That is clear support for mutations being largely delerious because what is known of them centers on disease and disorder. Indels are a major source of genetic defects, it's as simple as that.

You're right that I was confrontational first. But oh well. You did refer to Darwin: Darwin admitted that the gradual development of the eye seemed unlikely in the extreme. When it came to the brain he just said the smallest human brain is about the same size of the largest ape brain. We now know that brains are built by highly specific and conserved genes that do not respond well to mutations. and your first sentence was a clear quotemine. He was being rhetorical as much as he was foreseeing difficulties.

Look, it's not like natural selection is not a good explanation for a lot of things. It's just that when you get into things like the neural net it gets a whole lot more complicated. You are going to encounter these puzzles everytime you explore the theory of evolution. Natural selection as an explanation for humans evolving from apes is faulty on a lot of levels. The problem is that in Darwinism this is the primary mechanism for accumulating adaptive traits. If this does not explain a crucial adpatation then it's find another naturalistic mechanism or begin to consider the alternative.

I'm not saying creationism but there has to be a point where you abandon normative natural selection and start looking at other explanations. My problem is not with TOE per se, it's with Darwinism and especially in the human lineage. Nothing evolves like ape would have had to and you should recognize that whether you admit it or not.

How d'you like being dismissed as being merely semantical?

If it's a minor point I consider that a bonus.

Fact is that if indels can cause genetic defects, indels can also undo genetic defects. If a deletion of AG can cause a defect, then an insertion of AG can undo that defect. And the undoing of a defect from a wild-type is a beneficial mutation. For example:

Another example is the dramatic increase in the size of human brains compared with the brains of their ape cousins, according to Dr. Christopher A. Walsh, chief of genetics at Children's Hospital Boston. He helped identify a gene that, when mutated, causes children to be born with brains less than half the normal size -- comparable, in fact, to the size of a chimpanzee brain. What is remarkable about the disease, called microcephaly, is that it is not deadly. It is debilitating, but patients can learn to walk on their own and sometimes even speak a few words.



It seems likely, Walsh suggested, that changes in this one gene, long ago, may have helped humans develop larger brains. The gene does not appear to be involved in regulating other genes, but it shows how a relatively small change can have a dramatic effect.
​

http://www.boston.com/news/science/...ging_the_way_we_think_about_evolution/?page=3

Think about what you are reading here for a minute. This is a genetic defect resulting in a reduced brain size resulting in sever mental retardation.

A mutation in a human gene reproduces effects of the wild-type chimp gene, and so is a source of genetic defect; but this mutation is merely undoing the original mutation which changed the wild-type chimp gene into the human gene, which was a beneficial mutation.

You can assume this but demonstrating it is another thing altogether. Think what you like but there would be more then a few choice mutations. One area of divergance is the neural genes and sooner or later you are going to have to come to terms with that. Forget about the psuedogenes, this is the human brian we are talking about.

The last time I checked, argument from authority was also fallacious.

You missed the original point, Francis Bacon said that arguments from credulity were idols of the mind. I would think you would appreciate the words of the father of inductive method since modern science is based on it.​

 

[Smidlee]

Look, it's not like natural selection is not a good explanation for a lot of things.

IMO all natural selection is good for is wipe out the deformed and defected cause by mutation. Now supernatural-selection can explain a lot.

Think about what you are reading here for a minute. This is a genetic defect resulting in a reduced brain size resulting in sever mental retardation.

Also this article doesn't seem to mention anything about the children with this defect wanting to swing in trees or a greater desire for bananas.

 

[mark kennedy]

IMO all natural selection is good for is wipe out the deformed and defected cause by mutation.

That's my main point, this is what happens when changes in the neural genes produces an effect strong enough for natural selection to act. It results in things like mental retardation, Alzeheimer's, Parkinson's and brain tumors. There is still the problem of our supposed ape ancestors tripling their cranial capacity in a relativly short space of evolutionary time. Evolutionists still don't have a clue how it's possible but insist it's a scientific fact.

Now supernatural-selection can explain a lot. Also this article doesn't seem to mention anything about the children with this defect wanting to swing in trees or a greater desire for bananas.

We call it supernatural when God acts in time and space but that's just our perspective on it. For God this is perfectly normal, the fact that we don't know how he does certain things is completly irrelevant.

 

[shernren]

Simple explanations have been exhausted and apparently there is a scramble to explain divergence.

You appear to be short of free time and that's fine, so my response is to focus on this single segment where your misunderstanding appears to me to be both most severe and most easily corrected. Is that fine? We'll leave the conceptual wrangling for a better time and focus on basic comprehension errors.

You said you "didn't trust my sources". Well, I'm only citing a single source, which is the single source you also refer to in making this statement: Initial sequence of the chimpanzee genome and comparison with the human genome, Nature, 2005. I'm going to quote the segment in question with heavy formatting, including stripping footnote hyperlinks. Bold indicates topic sentences of paragraphs and italic indicates the section usually cited by mark, which will be pasted again on its own for clarity.

Genome-wide rates. We calculate the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%, confirming recent results from more limited studies. The differences between one copy of the human genome and one copy of the chimpanzee genome include both the sites of fixed divergence between the species and some polymorphic sites within each species. By correcting for the estimated coalescence times in the human and chimpanzee populations, we estimate that polymorphism accounts for 14–22% of the observed divergence rate and thus that the fixed divergence is

1.06% or less.


Nucleotide divergence rates are not constant across the genome, as has been seen in comparisons of the human and murid genomes. The average divergence in 1-Mb segments fluctuates with a standard deviation of 0.25% (coefficient of variation = 0.20), which is much greater than the 0.02% expected assuming a uniform divergence rate.

Regional variation in divergence could reflect local variation in either mutation rate or other evolutionary forces. Among the latter, one important force is genetic drift, which can cause substantial differences in divergence time across loci when comparing closely related species, as the divergence time for orthologues is the sum of two terms: t1, the time since speciation, and t2, the coalescence time for orthologues within the common ancestral population. Whereas t1 is constant across loci (

6–7 million years), t2 is a random variable that fluctuates across loci (with a mean that depends on population size and here may be on the order of 1–2 million years). However, because of historical recombination, the characteristic scale of such fluctuations will be on the order of tens of kilobases, which is too small to account for the variation observed for 1-Mb regions. Other potential evolutionary forces are positive or negative selection. Although it is more difficult to quantify the expected contributions of selection in the ancestral population, it is clear that the effects would have to be very strong to explain the large-scale variation observed across mammalian genomes. There is tentative evidence from in-depth analysis of divergence and diversity that natural selection is not the major contributor to the large-scale patterns of genetic variability in humans. For these reasons, we suggest that the large-scale variation in the human–chimpanzee divergence rate primarily reflects regional variation in mutation rate.
​

Now, when mark uses this quote, he normally draws attention to the emphasized part, consciously or not:

Although it is more difficult to quantify the expected contributions of selection in the ancestral population, it is clear that the effects would have to be very strong to explain the large-scale variation observed across mammalian genomes. There is tentative evidence from in-depth analysis of divergence and diversity that natural selection is not the major contributor to the large-scale patterns of genetic variability in humans. For these reasons, we suggest that the large-scale variation in the human–chimpanzee divergence rate primarily reflects regional variation in mutation rate.
​

to construct an argument by incredulity that since natural selection apparently does not explain "chimpanzee-human divergence", humans must have been specially created.

The problem is that we are not referring to overall divergence being higher than expected. We are referring to some areas of the genome experiencing less mutation than expected by a simple model, and some areas of the genome experiencing more mutation than expected by a simple model. The question now is not why these mutations have been fixed but why the spread?

To put it concretely: a simple model might predict that region A and region B should each have 12 fixed mutations. However, we actually find that region A has 8 mutations and region B has 17 mutations. The question is now why the difference? There are two possibilities:

1. Region A has a lower mutation rate than B.
2. Region A and Region B have the same mutation rate, but less mutations were fixed in Region A than in Region B, due to evolutionary forces.

This is what the pertinent topic sentence "Regional variation in divergence could reflect local variation in either mutation rate or other evolutionary forces" means. It may either be that mutation rates vary, or that mutation rates are constant but fixation rates vary.

The paragraph in question then goes on to examine the hypothesis that fixation rates vary: i.e., that each region has about the same number of mutations, but some have more fixed while others have less fixed. Genetic drift and natural selection are rejected as hypotheses of differing fixation rates. Hence, the remaining explanation is that mutation rates are different.

Note that all this says is that Region A (from above) experienced less mutations than Region B. But all the mutations in Region A were subsequently fixed by genetic drift and natural selection; all the mutations in Region B were subsequently fixed by genetic drift and natural selection. What natural selection "does not explain" is why there were less mutations in Region A than in Region B; but natural selection does explain why those mutations that were present were fixed in both those regions.

When analyzed properly, this simply is not the deathblow to human evolution you imagine it is.

 

[GenemZ]

Apparently we are only 96% similar to chimps now.

Funny.... If you look at all the posts in this forum?


You would find that they all are about 99.99% similar. Same fonts. Same background. Same format. Etc...

But? Guess what? They all express different ideas and concepts. According to statistics? We are all talking about the same thing. Yet, one thread's content can be worlds apart from another....

Playboy magazine is about 99.99% similar to Theology Today.

Grace and peace, GeneZ​

​

 

[Assyrian]

__________Playboy magazine
Theology Today

I make it only 12.5% similar,
possible 25% if the bo sequence has been turned around to give od

 

[GenemZ]

__________Playboy magazine
Theology Today

I make it only 12.5% similar,
possible 25% if the bo sequence has been turned around to give od

That is a perfect example for the very reason for endless debates. Avoiding admitting to when a point is made, by creating a clever diversion.

Its going to be nice to be in a resurrection body. So much evil and nonsense will have been eliminated. It gives me such hope.

And, the resurrection will not be achieved by evolution.

GeneZ
​

 

[Assyrian]

Is it a clever diversion to show the that actual similarity between two texts* is much smaller than the 99.99% you claim? But there is little reason for you to even read this reply if you believe it is 99.99% similar to your own post.

*or at least their titles, I am reluctant to go out and buy a copy of playboy, even for scientific research purposes.

 

[vossler]

Apparently we are only 96% similar to chimps now.

Our scientific understanding of Creation is, and forever will be, ever changing. Don't ever put your trust in something that isn't constant, trust in the Lord and His never changing Word then nothing will ever rattle you or cause one to doubt.

 

[rmwilliamsll]

Our scientific understanding of Creation is, and forever will be, ever changing. Don't ever put your trust in something that isn't constant, trust in the Lord and His never changing Word then nothing will ever rattle you or cause one to doubt.

don't ever read any Church history or introduction to Christian theology using an historical method. the truth will be too difficult to absorb with this attitude foremost in your mind. For the fact is that very determined and dedicated Christians have doubted, have been seriously rattled, and that the interpretation of Scripture is not a very consistent thing, not in the past, not even in the world today amongest Christians.

 

[vossler]

don't ever read any Church history or introduction to Christian theology using an historical method. the truth will be too difficult to absorb with this attitude foremost in your mind. For the fact is that very determined and dedicated Christians have doubted, have been seriously rattled, and that the interpretation of Scripture is not a very consistent thing, not in the past, not even in the world today amongest Christians.

Of course if we just see Scripture solely as mythological in nature we won't have to concern ourselves with the historicity of it.

Because the interpretation of Scripture has not always been consistent we're to treat it like science as an ever evolving study.

 

[rmwilliamsll]

in reply to:

Of course if we just see Scripture solely as mythological in nature we won't have to concern ourselves with the historicity of it.

Because the interpretation of Scripture has not always been consistent we're to treat it like science as an ever evolving study.

the context:
Our scientific understanding of Creation is, and forever will be, ever changing. Don't ever put your trust in something that isn't constant, trust in the Lord and His never changing Word then nothing will ever rattle you or cause one to doubt.

don't ever read any Church history or introduction to Christian theology using an historical method. the truth will be too difficult to absorb with this attitude foremost in your mind. For the fact is that very determined and dedicated Christians have doubted, have been seriously rattled, and that the interpretation of Scripture is not a very consistent thing, not in the past, not even in the world today amongest Christians.

Of course if we just see Scripture solely as mythological in nature we won't have to concern ourselves with the historicity of it.

Because the interpretation of Scripture has not always been consistent we're to treat it like science as an ever evolving study.

you miss the point, even among historical-grammatical hermeneutic using people there is a great deal of discussion about what the Scriptures mean. to try to anchor faith in a never changing interpretation ignores this fact, and neglects the painful suffering of many who have struggled with the issues. it strikes me as glib and ignorant to ignore these differences and the struggles of good strong believers to deal with them..

this is essentially name calling, i do not interpretation the first chapters of Genesis as mythology.

the fact remains that even among the various interpretative communities the meaning of Scripture has been and will continue to change. for it is after all a human endeavor to understand, interpretation does not just drop out of heaven complete and unchanging, but rather is the results of human effort and is tainted by human sin. and ought to be fixing that.

always reforming.

 

[Servant222]

Am I just sensitive, or are there several points in the last few posts that could have been made in a less aggressive way? I have no problem with contrary opinions, but don't think we need to make even subtle comments that some may view as being derogatory or inflammatory.

I think this is important because it would be unfortunate if people stop participating in these forums because they view the discussions as being too cantankerous.

I always assume that there are viewers out there who are reading some of this material and using it to try and determine what Christians and Christianity are all about.

 

[GenemZ]

Is it a clever diversion to show the that actual similarity between two texts* is much smaller than the 99.99% you claim? But there is little reason for you to even read this reply if you believe it is 99.99% similar to your own post.

See how much difference is manifested between us two? Even with such little difference in text?

Likewise.....

The LORD did not have to create a greatly diverse DNA for monkeys and man to make them vastly different in their being.

Besides, DNA is not to be found in the soul. The soul is immaterial and contains no DNA. And, it was the soul is what was created in God's image. The body from the elements of the earth for the body of man? That's only a vehicle for the soul while it lives in time and space. The is what has the DNA. And, man will not always have the same body. Yet, the soul remains the same.

If God put a human soul inside a monkey? You would have a man in expression, and an appearance that would end him in a freak show at a circus.

Or, a reporter for the Washington Post.

As always..... Grace and peace, GeneZ

 

[vossler]

you miss the point, even among historical-grammatical hermeneutic using people there is a great deal of discussion about what the Scriptures mean. to try to anchor faith in a never changing interpretation ignores this fact, and neglects the painful suffering of many who have struggled with the issues. it strikes me as glib and ignorant to ignore these differences and the struggles of good strong believers to deal with them.

There's always a great deal of discussion on the meaning of Scripture, that's human nature and there's nothing wrong with that. However, that should never be something we use as a crutch for not understanding and thereby giving us permission to change our interpretation to comply with human conjecture and speculation. We should be building upon the known knowledge of the truth of Scripture, not changing it. If I'm constantly looking at the foundation for cracks and flaws I'll be doing likewise for the rest of the structure and thereby missing the beauty and more importantly the meaning of all that it holds. Man now becomes the final arbitor and that is never good. There can never be anything glib or ignorant about doing that.

this is essentially name calling, i do not interpretation the first chapters of Genesis as mythology.

The problem is TEs are all over the map on this, some see it primarily as mythological and others see some historical elements. Except for the lack of consistency there's no consistency, which in my opinion can be quite convenient. So, let's be clear, I'm not trying to call you or anyone else a name, if you've interpreted my words as such I'm sorry. I'm just stating what I see and that is how TEs, as a means of not having to deal with the historicity of Scripture, conveniently see it as mythological.

the fact remains that even among the various interpretative communities the meaning of Scripture has been and will continue to change. for it is after all a human endeavor to understand, interpretation does not just drop out of heaven complete and unchanging, but rather is the results of human effort and is tainted by human sin. and ought to be fixing that.

Here's the bottom line, God and His Word never changes. If you wish to believe our interpretation of it should be everchanging you are free to do so, but I will not. This line of thinking goes completely against my beliefs and I will not entertain it. If He wants me to obey, I can't just go around picking a choosing what I wish to obey because my interpretation of His commands are in a constant flux.

My primary job as a Christian is to develop a personal relationship with my Lord and by doing so I will know what pleases Him so that I can better love Him. How can I get adequately know Him and thereby love Him if I don't thoroughly read and study His Word? It's just not possible! So, the easiest means of doing this is to spend time in His Word. That alone isn't enough though, we're also called to meditate on it day and night. This means it should become a part of us and we should be speaking it constantly because it is our source, our well spring if you will, of all that He wants us to know. Yet, that still isn't enough though because if we don't obey His Word it is all for naught. So, it is through this process that I will overcome my sins and all the extraneous human and satanic endeavors intent on distracting me from my mission.

 

[rmwilliamsll]

Here's the bottom line, God and His Word never changes. If you wish to believe our interpretation of it should be everchanging you are free to do so, but I will not. This line of thinking goes completely against my beliefs and I will not entertain it. If He wants me to obey, I can't just go around picking a choosing what I wish to obey because my interpretation of His commands are in a constant flux.

it is a fact that our interpretation does change.
to minimize this fact and to assert that you believe in the never changing, forever the same interpretation is simply to ignore history.

I'm part of the conservative reformed tradition. Even a hero of the faith like J.G.Machen, who taught roughly 80 years ago taught things which i no longer believe, nor does probably anyone in my church. In the same way, there are a few things that we believe are Biblical that he fought against and said were not Biblical. I simply do not understand this historical myopia on the part of so many modern day Christians, it seems that they wish to escape the past and believe that they believe like people have believed for 2K years. It simply is not true and minimizes the struggles of the church to reform and change it's ideas over the generations.

 

[Assyrian]

See how much difference is manifested between us two? Even with such little difference in text?

Likewise.....

The LORD did not have to create a greatly diverse DNA for monkeys and man to make them vastly different in their being.

Besides, DNA is not to be found in the soul. The soul is immaterial and contains no DNA. And, it was the soul is what was created in God's image. The body from the elements of the earth for the body of man? That's only a vehicle for the soul while it lives in time and space. The is what has the DNA. And, man will not always have the same body. Yet, the soul remains the same.

So is the difference between man and other apes because of a few % DNA or because the spirit God has created in us?

If you asked a gorilla It would probably consider itself very different from bonobos, orangs or spider monkeys. There is certainly a bigger genetic difference between a chimp and a spider monkey than there is between a chimp and us.

If God put a human soul inside a monkey? You would have a man in expression, and an appearance that would end him in a freak show at a circus.

Not if everyone else had the same mix of soul and simian.

Or, a reporter for the Washington Post.

As always..... Grace and peace, GeneZ

Cheers.

 

[vossler]

it is a fact that our interpretation does change. to minimize this fact and to assert that you believe in the never changing, forever the same interpretation is simply to ignore history.

Like I said, you're free to follow this line of thinking which allows our interpretations to be in a constant state of flux, I'm not. I'm very content in my belief because God provides absolutely no avenue or guidance for us to follow that would have our interpretation of Scripture or our beliefs to be in a constant state of change.

I simply do not understand this historical myopia on the part of so many modern day Christians, it seems that they wish to escape the past and believe that they believe like people have believed for 2K years. It simply is not true and minimizes the struggles of the church to reform and change it's ideas over the generations.

No escape required, I love history more than most people and find that it is many times our best teacher.

BTW, I have no problem what-so-ever with being narrow-minded when it comes to Scripture.