Neanderthal DNA
Sean Pitman M.D.
Neanderthal mitochondrial DNA (mtDNA) had been successfully recovered
and sequenced by Svante Pääbo and his team.25 Of course there were
statistical differences between Neanderthal DNA and the DNA of modern
humans. These differences were used to calculate the evolutionary
divergence of Neanderthals from a common ancestor to around 550,000 to
690,000 years ago. It is thought that Neanderthals then became
extinct without contributing mtDNA to the modern human genome. In
other words, Neanderthals were just one of many offshoots or splinter
groups that became extinct but who were not direct links to modern
humans in our evolutionary branch.
However, there are just a few problems with this theory. One problem
has come to the forefront with movies such as Jurassic Park and with
the publicity of the O.J. Simpson murder trial where DNA technology
played a prominent role. Some problems that were brought more clearly
to light by these media events is that DNA does not last very long.
It breaks down fairly rapidly depending on environmental factors.
Even under the most favorable conditions, many scientists believe that
DNA cannot remain identifiably intact beyond a few tens of thousands
of years. 27,28 In light of this fact, how could Neanderthal DNA
avoid decay over the "120,000 to 150,000" years that is the
hypothesized age of these bones? This seems to be quite a significant
problem. Of course, the reports of recovering DNA from amber that is
millions of years old are now being discounted because of this very
problem.29
Repeatability seems to be a real issue as well. Not only is it
difficult to confirm claims of ancient DNA recovery from amber
specimens, but mtDNA recovery from Neanderthals has only been done
three times. Others have found it very difficult to repeat Pääbo's
results. Since the scientific method is based on repeatability, the
whole issue of Neanderthal mtDNA and its implications comes into
serious question. Consider the following comment from Pääbo himself:
"Preserved Neandertal DNA is likely to be rare, and the DNA in the
type specimen [the 1856 Neander Valley Neandertal fossil] may result
from its unique preservation conditions. … Most Neandertal
specimens are therefore unlikely to contain amplifiable DNA. …"
30
Despite these problems, Pääbo et al. seem to have overcome them in
this particular case and presented their conclusions in the following
statement:
"The Neandertal sequence was compared to 994 contemporary human
mitochondrial lineages, i.e., distinct sequences occurring in one or
more individuals, found in 478 Africans, 510 Europeans, 494 Asians,
167 Native Americans and 20 individuals from Australia and Oceania.
Whereas these modern human sequences differ among themselves by an
average of 8.0 ± 3.l (range 1–24) substitutions, the difference
between the humans and the Neandertal sequence is 27.2 ± 2.2 (range
22–36) substitutions. Thus, the largest difference observed
between any two human sequences was two substitutions larger than the
smallest difference between a human and the Neandertal." 25
The conclusions drawn were as follows:
"When the comparison was extended to 16 common chimpanzee lineages,
the number of positions in common among the human and chimpanzee
sequences was reduced to 333. This reduced the number of human
lineages to 986. The average number of differences among humans is 8.0
± 3.0 (range 1–24), that between humans and the Neandertal, 25.6
± 2.2 (range 20–34), and that between humans and chimpanzees,
55.0 ± 3.0 (range 46–67). Thus, the average number of mtDNA
sequence differences between modern humans and the Neandertal is about
three times that among humans, but about half of that between modern
humans and modern chimpanzees.
To estimate the time when the most recent ancestral sequence
common to the Neandertal and modern human mtDNA sequences existed, we
used an estimated divergence date between humans and chimpanzees of
4–5 million years ago and corrected the observed sequence
differences for multiple substitutions at the same nucleotide site.
This yielded a date of 550,000 to 690,000 years before present for the
divergence of the Neandertal mtDNA and contemporary human mtDNAs. When
the age of the modern human mtDNA ancestor is estimated using the same
procedure, a date of 120,000 to 150,000 years is obtained, in
agreement with previous estimates. Although these dates rely on the
calibration point of the chimpanzee-human divergence and have errors
of unknown magnitude associated with them, they indicate that the age
of the common ancestor of the Neandertal sequence and modern human
sequences is about four times greater than that of the common ancestor
of modern human mtDNAs.
The Neandertal mtDNA sequence thus supports a scenario in which
modern humans arose recently in Africa as a distinct species and
replaced Neandertals with little or no interbreeding." 25
If mtDNA was in fact isolated from the Neanderthal bones, these
conclusions might seem reasonable until one considers a few more
facts. The Cell article itself noted that the range of sequence
differences for modern human mtDNA goes from 1 to 24 with an average
of 8 substitutions. The mtDNA sequence differences between modern
humans and the single Neanderthal fossil range from 22 to 36
substitutions, with the average being 27. In other words, the two
most different humans analyzed in this study, as far as mtDNA
substitutions are concerned, are different by 24 substitutions. The
closest that any human in this study was to the single specimen of
Neanderthal mtDNA was 22 substitutions. This means that there are
some people living today that are closer to Neanderthals in their
mtDNA sequencing than they are to some other modern human beings.
Someone might be found to be only 22 substitutions away from our
Neanderthal, but 24 substitutions away from his own next-door
neighbor. Interesting isn't it? If Neanderthals are classed as
separate species because of these differences, which one of our modern
human volunteers should be classify as a separate species? Perhaps
the one who had only 22 substitutions different from the Neanderthal?
Or, maybe his neighbor who had 24 substitutions away from him?
There have been attempts by popular scientists to describe exactly how
this mtDNA evidence turns Neanderthals into separate species. Some
describe it as a group of early Homo sapiens huddled around a fire.
Some are shoulder to shoulder while others, on the other side of the
fire might be several feet away... maybe even 24 feet away. However,
the average distance that any one person is from any other person is
just 8 feet. Now we notice a dark Neanderthal figure in the shadows
far from the fire. He averages 27 feet away from any given Homo
sapien huddled around the fire. Obviously therefore, he is an
outsider, a different species all together.
However closer inspection reveals that some of those huddled around
the fire are closer to the Neanderthal than they are to certain others
that are also huddled around the fire. Does that make them more
closely related to Neanderthals, who belong to a completely different
species, than to certain members of their own species? This sounds
rather silly does it not? And yet, this is what must be the obvious
conclusion. For example, what if we started with the Neanderthal
specimen and then picked a person at random out of a crowd. We might
get someone who is different by 24 substitutions from our Neanderthal
specimen. Now, we pick someone else out of the crowd who just so
happens to also be different by 24 substitutions from our Neanderthal
specimen and by 24 substitutions from our first human volunteer.
Which one is the new species? They are all equidistant from each
other. In order to visualize the problem, draw three dots on a piece
of paper, one for each of our two volunteers and the third dot for our
Neanderthal "volunteer." Make sure to draw each one on the paper
separated by 24 units of measure from each of the other two dots.
Now, pick the one that is the new species and the two that belong to
the same species. Maybe there are three separate species represented
here? However, all one would have to do to disprove this notion is
get two of the volunteers to "produce offspring" so to speak. If that
happened, the entire notion that a separation of 20 or so
substitutions makes for a new species, would have to be... well...
revised somewhat.
Why this problem has not been more publicly recognized seems rather
strange. I am sure that I am not the first one to wonder about this.
And yet, popular scientist seem not even to be aware that there is
this problem. It seems that the statistical averages of 8 and 27 are
so different that this squelches any suggestion that there might be a
problem. Using this average difference as a basis for their
conclusions, Kahn and Gibbons wrote in the journal Science that these
averages put Neanderthal out of the statistical range of modern human
variation.31
This statement is clearly misguided because not only are there humans
living today with wider separations between them than our Neanderthal
friend, but it is a statistical error or pitfall to compare many
different entities with just one entity. In other words, we do not
know what the Neanderthal mtDNA average is if there is just one
specimen. How then can we know if this one Neanderthal was not a
statistical outlier? How do we know that if we but had more
Neanderthal samples that the average would not be closer to that of
modern humans?
As it turns out, since the first sequence was obtained by Pääbo and
his team, there have been two more Neanderthals found who's mtDNA was
intact enough to sequence. The second sequence was done in 1999 on a
baby discovered in Mesmaiskaya Cave in south-western Russia. This
Neanderthal baby is thought to have died 29,000 years ago. The
sequence of this baby differed from the first sequence by 12
substitutions. The average number of substitutions between the second
Neanderthal mtDNA ("Baby M" for short) and a given human is 22 as
compared to 27 from the first Neanderthal sequence.46,47 In other
words, Baby M was "closer to the Homo sapien fire" than the first
shadowy Neanderthal. This means that some living humans might be even
closer to this second Neanderthal than they are to other living humans
by quite a fair margin. Unfortunately however, no figures for the
minimum, average, and maximum distances between the second Neanderthal
and modern humans was provided.
The third Neanderthal who's mtDNA was successfully sequenced was found
in a cave at Vindija, Croatia. In 2000, scientists announced the
mtDNA sequencing of this third Neanderthal specimen. This new
sequence fell within a 3.75% cluster of the first two sequences.48
Modern humans cluster at around 3.5%. This is a rather narrow level
of diversity when one compares these clusters to chimps (15%) and
gorillas (19%). Various human ethnic groups also have rather narrow
ranges of diversity in their mtDNA sequencing. Of course, the problem
still remains that some humans from certain of these ethic groups are
more closely "related" to Neanderthals than they are to certain other
living humans from other groups. The question remains as to who
should be classed as a separate species?
Maryellen Ruvolo (Harvard University) points out that the genetic
variation between the modern human and Neanderthal sequences is within
the range of other single species of primates. She goes on to say:
"… there isn’t a yardstick for genetic difference upon
which you can define a species." 31
Further confusion comes from the comments in the Cell article that
seem to indicate that Neanderthals are more closely related to the
ancestral "chimpanzee" than modern humans are. This might not have
been the actual intention of the authors, but one could easily get
confused by the wording of the article. The fact of the matter is
that the single specimen of Neanderthal mtDNA was actually farther
away from chimp mtDNA than humans are from chimp mtDNA substitutions.
Clearly then, Neanderthal DNA is no closer "related" to chimp DNA than
human DNA is. 32
Also, the idea that mtDNA mutations can be used as a molecular clock
have been recently called into question by the journal Science. As it
turns out, former ideas about the timing of this clock might be in
error by as much as "20-fold." The famous "Mitochondrial Eve" once
thought to be around 100,000 to 200,000 years old, might now have to
be revised to as young as "6,000" years old. 33,34
D. Melnick and G. Hoelzer (Columbia University) tested the assumptions
of mtDNA based phylogenic relationships and concluded:
"Our results suggest serious problems with use of mtDNA to estimate
'true' population genetic structure, to date cladogenic events, and in
some cases, to construct phylogenies." 35
Jonathan Marks (Yale University) declared mtDNA determined
relationships to be highly biased:
"Most analysis of mitochondrial DNA are so equivocal as to render a
clear solution impossible, the preferred phylogeny relying critically
on the choice of outgroup and clustering technique." 36
Given all of these findings, what seems most reasonable? Are
Neanderthals anything but human? It seems like they fall well within
human ethnic variation. How then can we say that, based on such
variations in mtDNA sequences that Neanderthals belong to a different
group or species than Homo sapiens?
Sean
Steve LaBonne
that there are a lot more copies of mitochondrial than of nuclear DNA in
each cell, and that the sequences being compared are very short. The
Neanderthal woek possesses two characteristics crucial to verufiying its
accuracy: 1) at least one of the sequences has been duplicated via a sample
sent to a second lab, helping to rule out laboratory contamination; 2) the
_three_ available Neanderthal mtDNA sequences (you appear to be unaware that
there has been oither work besides the Paabo lab's)
cluster rather closely with each other but are quite different from any
modern modern sequences.
http://www.promega.com/profiles/402/ProfilesinDNA_402_09.pdf
I would not be surprised to hear that there are qualified scientists who
still have their doubts; nonetheless, I'm afraid your attempt at criticism
is neither well-informed nor cogent (neither OJ nor Jurassic Peak have
anything to do with the matter.)
Dunno
Thought experiment. Take a human with Robertsonian Translocation
and compare the altered segment with DNA from humans without
the translocation. Next compare with chimpanzee DNA from the
same segment. Compare the chimp to humans with the translocation
and also those without.
Isn't selective harvesting of data fun?
-
True adj. 1 (a) Stedfast, loyal. (b) Honest, just.
2 Qualifier for one's beliefs.
False adj. 1 Not genuine
2 (a) Intentionally untrue. (b) Intended to mislead.
3 Qualifier for others' beliefs.
Louann Miller
<labo...@lycos.com> wrote:
> (neither OJ nor Jurassic Peak have
>anything to do with the matter.)
(innocent wide-eyed look) Was that the mini-series that begins with a
dead velociraptor being found wrapped in plastic?
Louann
Harlequin
news:fd67d42a.02102...@posting.google.com:
[snip]
> The third Neanderthal who's mtDNA was successfully sequenced was found
> in a cave at Vindija, Croatia. In 2000, scientists announced the
> mtDNA sequencing of this third Neanderthal specimen. This new
> sequence fell within a 3.75% cluster of the first two sequences.48
> Modern humans cluster at around 3.5%. This is a rather narrow level
> of diversity when one compares these clusters to chimps (15%) and
> gorillas (19%). Various human ethnic groups also have rather narrow
> ranges of diversity in their mtDNA sequencing. Of course, the problem
> still remains that some humans from certain of these ethic groups are
> more closely "related" to Neanderthals than they are to certain other
> living humans from other groups. The question remains as to who
> should be classed as a separate species?
[snip]
This is not true. The mtDNA for the Neandertals was equally distant
from the various groups of humans.
From the _Nature_ publication of the second Neandertal individual:
The Feldhofer and Mezmaiskaya Neanderthals were separated
geographically by over 2,500 km. Given that these two individuals
contained closely related mtDNA, which is phylogenetically distinct
from modern humans, and displays only a moderate level of sequence
diversity compared with some primates13, these data provide further
support for the hypothesis of a very low gene flow between the
Neanderthals and modern humans. In particular, these data reduce
the likelihood that Neanderthals contained enough mtDNA sequence
diversity to encompass modern human diversity.
The 'out-of-Africa' hypothesis for the origin of modern humans
predicts equal distances between the Neanderthal sequences and
all modern sequences. We observed this in our analysis--the
average pairwise differences between the Neanderthals and 300
randomly selected Africans, Mongoloids and Caucasoids were
calculated to be 23.09+/-2.86, 23.27+/-4.06 and 25.45+/-3.27,
respectively.
http://www.nature.com/cgi-
taf/DynaPage.taf?file=/nature/journal/v404/n6777/full/404490a0_fs.html
The third Neandertal further supported this. See Chris Stringer's
comments at
http://news.bbc.co.uk/1/hi/sci/tech/967119.stm
--
Anti-spam: replace "usenet" with "harlequin2"
Ron Okimoto
"Sean Pitman M.D." wrote:
This is just another one of your crappy views of reality. I don't have
time to tell you where you are obviously wrong, but you have wasted quite
a bit of time for no reason. Just read the papers on Neandertal DNA.
You can't find a single one that claims to get DNA from 120,000 year old
Neandertal fossils. What you do find is that bones from warmer climates
no matter what their age are less useful to these analysis than the bones
from Europe. Conditions have a lot to do with preservation.
You seem to miss the point of the analysis. How you can claim that
certain Neandertal sequences are closer to modern humans using your
method is beyond good sense and reason. Find out how these analyses are
really done. All Neandertal mitochondrial sequences fall outside the
range of modern humans, but they do group with each other. This just
means that all Neandertals that have been sequenced are more closely
related to each other than they are to any extant human. They are
related to us, they fall between modern humans and chimps. What a waste
of a brain. You seemed to have some promise in the beginning, but you
are becoming lamer as time goes on. You must realize at some level that
the reason for this is because your position is so weak that trying to
support it with propaganda tracts like these makes you look pretty
stupid.
Ron Okimoto
zoe_althrop
is there any way to be sure that the DNA did not arise from the
flaking off of cells from the present-day human Neanderthal? Do we
have any eyewitnesses to the process? Not that they can necessarily
be believed, I guess.
>
>
>Despite these problems, Pääbo et al. seem to have overcome them in
>this particular case and presented their conclusions in the following
>statement:
>
>
>
>"The Neandertal sequence was compared to 994 contemporary human
>mitochondrial lineages, i.e., distinct sequences occurring in one or
>more individuals, found in 478 Africans, 510 Europeans, 494 Asians,
>167 Native Americans and 20 individuals from Australia and Oceania.
>Whereas these modern human sequences differ among themselves by an
>average of 8.0 ± 3.l (range 1–24) substitutions, the difference
>between the humans and the Neandertal sequence is 27.2 ± 2.2 (range
>22–36) substitutions. Thus, the largest difference observed
>between any two human sequences was two substitutions larger than the
>smallest difference between a human and the Neandertal." 25
>
>
>
>The conclusions drawn were as follows:
>
>
>
>"When the comparison was extended to 16 common chimpanzee lineages,
>the number of positions in common among the human and chimpanzee
>sequences was reduced to 333. This reduced the number of human
>lineages to 986. The average number of differences among humans is 8.0
>± 3.0 (range 1–24), that between humans and the Neandertal, 25.6
>± 2.2 (range 20–34), and that between humans and chimpanzees,
>55.0 ± 3.0 (range 46–67). Thus, the average number of mtDNA
>sequence differences between modern humans and the Neandertal is about
>three times that among humans, but about half of that between modern
>humans and modern chimpanzees.
fascinating.
> To estimate the time when the most recent ancestral sequence
>common to the Neandertal and modern human mtDNA sequences existed, we
>used an estimated divergence date between humans and chimpanzees of
>4–5 million years ago and corrected the observed sequence
>differences for multiple substitutions at the same nucleotide site.
>This yielded a date of 550,000 to 690,000 years before present for the
>divergence of the Neandertal mtDNA and contemporary human mtDNAs. When
>the age of the modern human mtDNA ancestor is estimated using the same
>procedure, a date of 120,000 to 150,000 years is obtained, in
>agreement with previous estimates. Although these dates rely on the
>calibration point of the chimpanzee-human divergence and have errors
>of unknown magnitude associated with them, they indicate that the age
>of the common ancestor of the Neandertal sequence and modern human
>sequences is about four times greater than that of the common ancestor
>of modern human mtDNAs.
"unknown magnitude" did you say? Is that true?
> The Neandertal mtDNA sequence thus supports a scenario in which
>modern humans arose recently in Africa as a distinct species and
>replaced Neandertals with little or no interbreeding." 25
>
>
>
>If mtDNA was in fact isolated from the Neanderthal bones, these
>conclusions might seem reasonable until one considers a few more
>facts. The Cell article itself noted that the range of sequence
>differences for modern human mtDNA goes from 1 to 24 with an average
>of 8 substitutions. The mtDNA sequence differences between modern
>humans and the single Neanderthal fossil range from 22 to 36
>substitutions, with the average being 27. In other words, the two
>most different humans analyzed in this study, as far as mtDNA
>substitutions are concerned, are different by 24 substitutions. The
>closest that any human in this study was to the single specimen of
>Neanderthal mtDNA was 22 substitutions. This means that there are
>some people living today that are closer to Neanderthals in their
>mtDNA sequencing than they are to some other modern human beings.
>Someone might be found to be only 22 substitutions away from our
>Neanderthal, but 24 substitutions away from his own next-door
>neighbor. Interesting isn't it? If Neanderthals are classed as
>separate species because of these differences, which one of our modern
>human volunteers should be classify as a separate species? Perhaps
>the one who had only 22 substitutions different from the Neanderthal?
>Or, maybe his neighbor who had 24 substitutions away from him?
chances are that my neighbor has Neanderthal mtDNA -- or maybe I do.
Seems like what this is boiling down to is that they found the bones
of a homo sapien and called it by a new name, "Neanderthal."
>
>There have been attempts by popular scientists to describe exactly how
>this mtDNA evidence turns Neanderthals into separate species. Some
>describe it as a group of early Homo sapiens huddled around a fire.
>Some are shoulder to shoulder while others, on the other side of the
>fire might be several feet away... maybe even 24 feet away. However,
>the average distance that any one person is from any other person is
>just 8 feet. Now we notice a dark Neanderthal figure in the shadows
>far from the fire. He averages 27 feet away from any given Homo
>sapien huddled around the fire. Obviously therefore, he is an
>outsider, a different species all together.
how interesting!
whew!
>Also, the idea that mtDNA mutations can be used as a molecular clock
>have been recently called into question by the journal Science. As it
>turns out, former ideas about the timing of this clock might be in
>error by as much as "20-fold." The famous "Mitochondrial Eve" once
>thought to be around 100,000 to 200,000 years old, might now have to
>be revised to as young as "6,000" years old. 33,34
>
>D. Melnick and G. Hoelzer (Columbia University) tested the assumptions
>of mtDNA based phylogenic relationships and concluded:
>
>
>
>"Our results suggest serious problems with use of mtDNA to estimate
>'true' population genetic structure, to date cladogenic events, and in
>some cases, to construct phylogenies." 35
>
>
>
>Jonathan Marks (Yale University) declared mtDNA determined
>relationships to be highly biased:
>
>
>
>"Most analysis of mitochondrial DNA are so equivocal as to render a
>clear solution impossible, the preferred phylogeny relying critically
>on the choice of outgroup and clustering technique." 36
>
>
>
>Given all of these findings, what seems most reasonable? Are
>Neanderthals anything but human? It seems like they fall well within
>human ethnic variation. How then can we say that, based on such
>variations in mtDNA sequences that Neanderthals belong to a different
>group or species than Homo sapiens?
>
>
>Sean
>
An excellent, excellent post, Dr. Pitman. You made it very clear to
this lay person. Thanks for the thoughtful critique.
hallooo, Adam -- I vote for this as POTM.
----
zoe
zoe_althrop
impressive response here.
>I don't have
>time to tell you where you are obviously wrong,
too bad. I might have learned something from you, too, from another
perspective. So far Dr. Sean is ahead.
> but you have wasted quite
>a bit of time for no reason.
not at all. I have learned a lot from him already.
> Just read the papers on Neandertal DNA.
>You can't find a single one that claims to get DNA from 120,000 year old
>Neandertal fossils. What you do find is that bones from warmer climates
>no matter what their age are less useful to these analysis than the bones
>from Europe. Conditions have a lot to do with preservation.
>
>You seem to miss the point of the analysis. How you can claim that
>certain Neandertal sequences are closer to modern humans using your
>method is beyond good sense and reason. Find out how these analyses are
>really done. All Neandertal mitochondrial sequences
ALL? All five or six of them?
> fall outside the
>range of modern humans, but they do group with each other. This just
>means that all Neandertals that have been sequenced are more closely
>related to each other than they are to any extant human.
large universe to sample here -- wow.
>They are
>related to us, they fall between modern humans and chimps. What a waste
>of a brain. You seemed to have some promise in the beginning, but you
>are becoming lamer as time goes on. You must realize at some level that
>the reason for this is because your position is so weak that trying to
>support it with propaganda tracts like these makes you look pretty
>stupid.
do you get out often into the social circles of the real world, Ron
Okimoto? Doesn't sound like it. Either that, or you've forgotten how
to interact with your peers.
----
zoe
Mark VandeWettering
The fact that Ron may have had a bad day and is in a crappy mood is not
evidence that Pitman is correct. Given your performance in other threads,
the idea that you might learn something seems far-fetched as well.
>> but you have wasted quite
>>a bit of time for no reason.
> not at all. I have learned a lot from him already.
It's a pity that you only choose to learn from teachers of dubious quality.
>> Just read the papers on Neandertal DNA.
>>You can't find a single one that claims to get DNA from 120,000 year old
>>Neandertal fossils. What you do find is that bones from warmer climates
>>no matter what their age are less useful to these analysis than the bones
>>from Europe. Conditions have a lot to do with preservation.
>>
>>You seem to miss the point of the analysis. How you can claim that
>>certain Neandertal sequences are closer to modern humans using your
>>method is beyond good sense and reason. Find out how these analyses are
>>really done. All Neandertal mitochondrial sequences
>
> ALL? All five or six of them?
Yes.
>> fall outside the
>>range of modern humans, but they do group with each other. This just
>>means that all Neandertals that have been sequenced are more closely
>>related to each other than they are to any extant human.
>
> large universe to sample here -- wow.
We do have pretty good ideas as to the limits of variability in modern
humans. All existing Neanderthal sequences fall outside those limits.
>>They are
>>related to us, they fall between modern humans and chimps. What a waste
>>of a brain. You seemed to have some promise in the beginning, but you
>>are becoming lamer as time goes on. You must realize at some level that
>>the reason for this is because your position is so weak that trying to
>>support it with propaganda tracts like these makes you look pretty
>>stupid.
>
> do you get out often into the social circles of the real world, Ron
> Okimoto? Doesn't sound like it. Either that, or you've forgotten how
> to interact with your peers.
Peers?
Who are Ron's peers in this conversation?
Mark
>
> ----
> zoe
>
zoe_althrop
<wett...@attbi.com> wrote:
>> On Sat, 26 Oct 2002 00:35:49 +0000 (UTC), Ron Okimoto
>><roki...@uark.edu> wrote:
snip>
>>>I don't have
>>>time to tell you where you are obviously wrong,
>>
>> too bad. I might have learned something from you, too, from another
>> perspective. So far Dr. Sean is ahead.
>
>The fact that Ron may have had a bad day and is in a crappy mood is not
>evidence that Pitman is correct.
Ron must have many bad days, then. I've seen this kind of response
from him before...a curmudgeon, if I ever saw one.
>Given your performance in other threads,
>the idea that you might learn something seems far-fetched as well.
as an eyewitness to my threads, you will have to be taken with a cup
o' salt, Mark -- based on your approach to eyewitnesses.
>>> but you have wasted quite
>>>a bit of time for no reason.
>
>> not at all. I have learned a lot from him already.
>
>It's a pity that you only choose to learn from teachers of dubious quality.
please note that my learning is as a result of scientific data,
thoughtfully discussed. I think I can judge the quality of my
teachers for myself, thank you.
>>> Just read the papers on Neandertal DNA.
>>>You can't find a single one that claims to get DNA from 120,000 year old
>>>Neandertal fossils. What you do find is that bones from warmer climates
>>>no matter what their age are less useful to these analysis than the bones
>>>from Europe. Conditions have a lot to do with preservation.
>>>
>>>You seem to miss the point of the analysis. How you can claim that
>>>certain Neandertal sequences are closer to modern humans using your
>>>method is beyond good sense and reason. Find out how these analyses are
>>>really done. All Neandertal mitochondrial sequences
>>
>> ALL? All five or six of them?
>
>Yes.
that's not good enough, and you know it, Mark.
>
>>> fall outside the
>>>range of modern humans, but they do group with each other. This just
>>>means that all Neandertals that have been sequenced are more closely
>>>related to each other than they are to any extant human.
>>
>> large universe to sample here -- wow.
>
>We do have pretty good ideas as to the limits of variability in modern
>humans.
where did these ideas come from? Which eyewitnesses? Can they be
trusted?
> All existing Neanderthal sequences fall outside those limits.
all four or five of them, right. I'm impressed by your
four-person-high mountains of evidence.
>>>They are
>>>related to us, they fall between modern humans and chimps. What a waste
>>>of a brain. You seemed to have some promise in the beginning, but you
>>>are becoming lamer as time goes on. You must realize at some level that
>>>the reason for this is because your position is so weak that trying to
>>>support it with propaganda tracts like these makes you look pretty
>>>stupid.
>>
>> do you get out often into the social circles of the real world, Ron
>> Okimoto? Doesn't sound like it. Either that, or you've forgotten how
>> to interact with your peers.
>
>Peers?
>
>Who are Ron's peers in this conversation?
sorry, I was trying to be kind to him. He doesn't belong to Dr.
Pitman's peer group, evidently.
----
zoe
Pokemoto
>Path:
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>From: muz...@aol.com (zoe_althrop)
>Newsgroups: talk.origins
>Date: Sat, 26 Oct 2002 01:56:42 +0000 (UTC)
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>
>On Sat, 26 Oct 2002 01:41:02 +0000 (UTC), Mark VandeWettering
><wett...@attbi.com> wrote:
>
>>> On Sat, 26 Oct 2002 00:35:49 +0000 (UTC), Ron Okimoto
>>><roki...@uark.edu> wrote:
>
>snip>
>
>>>>I don't have
>>>>time to tell you where you are obviously wrong,
>>>
>>> too bad. I might have learned something from you, too, from another
>>> perspective. So far Dr. Sean is ahead.
>>
>>The fact that Ron may have had a bad day and is in a crappy mood is not
>>evidence that Pitman is correct.
>
>Ron must have many bad days, then. I've seen this kind of response
>from him before...a curmudgeon, if I ever saw one.
Zoe, you are just showing yourself to be in outer space somewhere. Think back,
I'm the one that tried to patiently correct your misconceptions. I have even
defended your feeble attempts when you first came here, and it seemed like you
had some honest questions. You can probably do a Google search from those
early days and see that I was one of the guys that came out against the first
brutal lashings that you were given because I thought that they were being
unfair. I have never called the junk that you come up with "crappy" as far as
I can recall. I just gave up trying to educate you a very long time ago. I
only castigate the people that I think should know better. This group never
included you.
>
>>Given your performance in other threads,
>>the idea that you might learn something seems far-fetched as well.
>
>as an eyewitness to my threads, you will have to be taken with a cup
>o' salt, Mark -- based on your approach to eyewitnesses.
>
>>>> but you have wasted quite
>>>>a bit of time for no reason.
>>
>>> not at all. I have learned a lot from him already.
>>
>>It's a pity that you only choose to learn from teachers of dubious quality.
>
>please note that my learning is as a result of scientific data,
>thoughtfully discussed. I think I can judge the quality of my
>teachers for myself, thank you.
Obviously you are mistaken if you can't see what is wrong with what Sean is
dishing out.
Why is it that you think that what Sean writes is OK, but nothing anyone writes
correcting your misconceptions about isochrons seems to register with you?
>
>>>> Just read the papers on Neandertal DNA.
>>>>You can't find a single one that claims to get DNA from 120,000 year old
>>>>Neandertal fossils. What you do find is that bones from warmer climates
>>>>no matter what their age are less useful to these analysis than the bones
>>>>from Europe. Conditions have a lot to do with preservation.
>>>>
>>>>You seem to miss the point of the analysis. How you can claim that
>>>>certain Neandertal sequences are closer to modern humans using your
>>>>method is beyond good sense and reason. Find out how these analyses are
>>>>really done. All Neandertal mitochondrial sequences
>>>
>>> ALL? All five or six of them?
>>
>>Yes.
>
>that's not good enough, and you know it, Mark.
What any sane person would realize is that just one Neandertal sequence that
falls well outside of the variation found in extant humans is a very large
problem for people like yourself that think that everyone was created just a
few thousand years ago. Are Neandertals human? Are they some other creation?
Why aren't they mentioned in the Bible?
>
>>
>>>> fall outside the
>>>>range of modern humans, but they do group with each other. This just
>>>>means that all Neandertals that have been sequenced are more closely
>>>>related to each other than they are to any extant human.
>>>
>>> large universe to sample here -- wow.
>>
>>We do have pretty good ideas as to the limits of variability in modern
>>humans.
>
>where did these ideas come from? Which eyewitnesses? Can they be
>trusted?
We have sequences for thousands of humans from all the different continents.
It is a fact that the Neandertal sequences fall outside of the variation that
we have observed. No, we probably never will have the DNA sequences for the
billions of people that currently exist, but if you are willing to fund such a
study I'm sure that you will find a group of researchers that would be willing
to sequence much larger sample sizes.
How do you think that you cross check for contamination? My wife worked in a
lab where they were sequencing a lot of human D-loop sequences looking into the
origins of native Americans. They all knew what haplotype they were. I'm sure
that the people doing the Neandertal work know that they do not have Neandertal
type mitochondrial DNA to contaminate the samples with.
You could do this research yourself if you don't trust the people doing it.
You don't have to have any evolutionary conceptions to just go out and find out
what exists out there. Do you think that the automated DNA sequencers are
biased and only give the results that we want?
>
>> All existing Neanderthal sequences fall outside those limits.
>
>all four or five of them, right. I'm impressed by your
>four-person-high mountains of evidence.
Considering the evidence that you have, it is a mountain, isn't it? Explain
the evidence that we have. Why complain that we don't have enough if it is
enough to say that you are full of baloney. Give an explanation for the
Neandertal sequences that is consistent with your model. If you can't explain
a couple of sequences, what makes you think that you could explain 10 or a
hundred? Why do you think that you have a chance of coming up with something
that would negate the results when they come from different countries and from
fossils from different time periods?
>
>>>>They are
>>>>related to us, they fall between modern humans and chimps. What a waste
>>>>of a brain. You seemed to have some promise in the beginning, but you
>>>>are becoming lamer as time goes on. You must realize at some level that
>>>>the reason for this is because your position is so weak that trying to
>>>>support it with propaganda tracts like these makes you look pretty
>>>>stupid.
>>>
>>> do you get out often into the social circles of the real world, Ron
>>> Okimoto? Doesn't sound like it. Either that, or you've forgotten how
>>> to interact with your peers.
>>
>>Peers?
>>
>>Who are Ron's peers in this conversation?
>
>sorry, I was trying to be kind to him. He doesn't belong to Dr.
>Pitman's peer group, evidently.
>
>----
>zoe
No, Pitman isn't a peer of mine. You know this as well as I do. He is just a
well educated person that would rather use his intellect to obfuscate the
issues instead of trying to learn something about nature. You would probably
know why he does this better than I would.
Ron Okimoto
Mark VandeWettering
> is there any way to be sure that the DNA did not arise from the
> flaking off of cells from the present-day human Neanderthal?
Chez Watt?
Mark VandeWettering
> On Sat, 26 Oct 2002 01:41:02 +0000 (UTC), Mark VandeWettering
><wett...@attbi.com> wrote:
>
>>> On Sat, 26 Oct 2002 00:35:49 +0000 (UTC), Ron Okimoto
>>><roki...@uark.edu> wrote:
>
> snip>
>
>>>>I don't have
>>>>time to tell you where you are obviously wrong,
>>>
>>> too bad. I might have learned something from you, too, from another
>>> perspective. So far Dr. Sean is ahead.
>>
>>The fact that Ron may have had a bad day and is in a crappy mood is not
>>evidence that Pitman is correct.
>
> Ron must have many bad days, then. I've seen this kind of response
> from him before...a curmudgeon, if I ever saw one.
Indeed. I've been accused of such myself. Being accused of being
a curmudgeon is not a refutation of the curmudgeon's arguments.
>>Given your performance in other threads,
>>the idea that you might learn something seems far-fetched as well.
>
> as an eyewitness to my threads, you will have to be taken with a cup
> o' salt, Mark -- based on your approach to eyewitnesses.
As amusing as the your endless lack of comprehension about isochrons have
been, they have not illustrated any ability for you to comprehend anything.
>>>> but you have wasted quite
>>>>a bit of time for no reason.
>>
>>> not at all. I have learned a lot from him already.
>>
>>It's a pity that you only choose to learn from teachers of dubious quality.
>
> please note that my learning is as a result of scientific data,
> thoughtfully discussed.
No, it isn't.
> I think I can judge the quality of my
> teachers for myself, thank you.
You can. You just exhibit the same level of competence in that regard
as you have in other threads.
>>>> Just read the papers on Neandertal DNA.
>>>>You can't find a single one that claims to get DNA from 120,000 year old
>>>>Neandertal fossils. What you do find is that bones from warmer climates
>>>>no matter what their age are less useful to these analysis than the bones
>>>>from Europe. Conditions have a lot to do with preservation.
>>>>
>>>>You seem to miss the point of the analysis. How you can claim that
>>>>certain Neandertal sequences are closer to modern humans using your
>>>>method is beyond good sense and reason. Find out how these analyses are
>>>>really done. All Neandertal mitochondrial sequences
>>>
>>> ALL? All five or six of them?
>>
>>Yes.
>
> that's not good enough, and you know it, Mark.
All available ones fall outside. All of them. When we have more of them,
there might be something else to discuss.
>>>> fall outside the
>>>>range of modern humans, but they do group with each other. This just
>>>>means that all Neandertals that have been sequenced are more closely
>>>>related to each other than they are to any extant human.
>>>
>>> large universe to sample here -- wow.
>>
>>We do have pretty good ideas as to the limits of variability in modern
>>humans.
>
> where did these ideas come from? Which eyewitnesses? Can they be
> trusted?
Science doesn't rely on eyewitness testimony Zoe.
>> All existing Neanderthal sequences fall outside those limits.
>
> all four or five of them, right. I'm impressed by your
> four-person-high mountains of evidence.
I frankly don't care what you are impressed by Zoe. Your capacity for
discrimination is not keen.
>>>>They are
>>>>related to us, they fall between modern humans and chimps. What a waste
>>>>of a brain. You seemed to have some promise in the beginning, but you
>>>>are becoming lamer as time goes on. You must realize at some level that
>>>>the reason for this is because your position is so weak that trying to
>>>>support it with propaganda tracts like these makes you look pretty
>>>>stupid.
>>>
>>> do you get out often into the social circles of the real world, Ron
>>> Okimoto? Doesn't sound like it. Either that, or you've forgotten how
>>> to interact with your peers.
>>
>>Peers?
>>
>>Who are Ron's peers in this conversation?
>
> sorry, I was trying to be kind to him. He doesn't belong to Dr.
> Pitman's peer group, evidently.
I'm sure he views that with great relief.
Mark
>
> ----
> zoe
>
Sverker Johansson
Not really. Modern-DNA contamination is a genuine concern in
paleoDNA analysis, though expressed in somewhat flaky terms here,
and there have been some embarrassments in the past.
But we have learnt to take rather extreme precautions:
Analysis of ancient DNA is typically done in "virgin" labs, where no related
modern species have ever been analysed. In the case of human relatives,
a common precaution is to sequence the DNA of everybody who works
with the samples, and compare with the paleo-sequence.
I'm fairly sure that Pääbo's team did all this. None of them is
a present-day Neanderthal.
--
Best regards, HLK, Physics
Sverker Johansson U of Jonkoping
----------------------------------------------
WAR IS PEACE
FREEDOM IS SLAVERY
IGNORANCE IS STRENGTH - adapted from
CREATIONISM IS SCIENCE George Orwell
Mark VandeWettering
> Mark VandeWettering wrote:
>>
>> In article <3db9e545...@news-server.cfl.rr.com>, zoe_althrop wrote:
>>
>> > is there any way to be sure that the DNA did not arise from the
>> > flaking off of cells from the present-day human Neanderthal?
>>
>> Chez Watt?
>
> Not really. Modern-DNA contamination is a genuine concern in
> paleoDNA analysis, though expressed in somewhat flaky terms here,
> and there have been some embarrassments in the past.
> But we have learnt to take rather extreme precautions:
I'm sorry, I know I am not giving Zoe any credit for subtlety, but I
actually not sure that she is aware that there are no present-day human
Neanderthals.
> Analysis of ancient DNA is typically done in "virgin" labs, where no related
> modern species have ever been analysed. In the case of human relatives,
> a common precaution is to sequence the DNA of everybody who works
> with the samples, and compare with the paleo-sequence.
>
> I'm fairly sure that Pääbo's team did all this. None of them is
> a present-day Neanderthal.
If modern humans contaminated ancient DNA specimens, we would expect to see
the results of the DNA tests strongly clustering with modern humans, not
disjoint from them, no?
Mark
Rob May
"Mark VandeWettering" <wett...@attbi.com> wrote in message
news:slrnark7g1.1...@keck.vandewettering.net...
Sverker Johansson
>
> In article <3DBA4543...@hlk.no.hj.spam.se>, Sverker Johansson wrote:
> > Mark VandeWettering wrote:
> >>
> >> In article <3db9e545...@news-server.cfl.rr.com>, zoe_althrop wrote:
> >>
> >> > is there any way to be sure that the DNA did not arise from the
> >> > flaking off of cells from the present-day human Neanderthal?
> >>
> >> Chez Watt?
> >
> > Not really. Modern-DNA contamination is a genuine concern in
> > paleoDNA analysis, though expressed in somewhat flaky terms here,
> > and there have been some embarrassments in the past.
> > But we have learnt to take rather extreme precautions:
>
> I'm sorry, I know I am not giving Zoe any credit for subtlety, but I
> actually not sure that she is aware that there are no present-day human
> Neanderthals.
I'm not sure either. But there is a Swedish proverb "Even a blind hen
occasionally finds a grain." Zoe produces quite enough unambiguous
nonsense that we don't need to look for CW among the stuff that _might_
be sensible.
> > Analysis of ancient DNA is typically done in "virgin" labs, where no related
> > modern species have ever been analysed. In the case of human relatives,
> > a common precaution is to sequence the DNA of everybody who works
> > with the samples, and compare with the paleo-sequence.
> >
> > I'm fairly sure that Pääbo's team did all this. None of them is
> > a present-day Neanderthal.
>
> If modern humans contaminated ancient DNA specimens, we would expect to see
> the results of the DNA tests strongly clustering with modern humans, not
> disjoint from them, no?
True. Furthermore, the fact that several independent analyses of different
Neanderthal specimens in different labs cluster with each other is strong
evidence that it isn't just contamination.
June
Jon Fleming
wrote:
>chances are that my neighbor has Neanderthal mtDNA -- or maybe I do.
>Seems like what this is boiling down to is that they found the bones
>of a homo sapien and called it by a new name, "Neanderthal."
Please present supporting data.
Sean Pitman M.D.
Neanderthals and other "early hominids" further at:
Dunno
Peeked at your page. A mined quote:
"Thus, the largest difference observed between any two human
sequences was two substitutions larger than the
smallest difference between a human and the Neandertal."
Krings, M., Stone, A., Schmitz, R.W., Krainitzki, H., Stoneking, M. and
Pbo,
S., 1997. Neandertal DNA sequences and the origin of modern humans. Cell,
90:19.30
A more recent article with input from some of the same
authors is at
http://www.eva.mpg.de/genetics/evgen/Krings_DNAseqProc1999.pdf
Something that may have not been included in the article you
cite, is that differences among the 9 chimp/bonobo
samples in the study were between 1 and 81 differences.
Differences between humans and bonobos/chimps used in
the study ranged from 78 to 113 differences. Note that
the lower range of human - chimp/bonobo differences fall
within the extremes of the differences amongst the chimp/bonobos.
Unfortunately, this is inconvenient for your argument wrt to
Neandertal MtDNA. Now that more detail is available in a more
recent article, shouldn't you update your page?
gen2rev
[snip]
Did you actually read the paper this purported "quote" is from? (Krings
et al. 1997. Neandertal DNA sequences and the origin of modern humans.
Cell, 90:19–30) You've taken three different paragraphs from pages
24-25, 25, and 27 and strung them all together. But these quotes are all
available on this page at Answers In Genesis:
http://www.answersingenesis.org/docs/4218tj_v12n1.asp
In fact, a lot of the material you use in this post is available on that
page.
[snip the rest]
Dunno
On Sat, 26 Oct 2002, zoe_althrop wrote:
>
>
> On Fri, 25 Oct 2002 16:42:30 +0000 (UTC), Sean...@juno.com (Sean
> Pitman M.D.) wrote:
>
> >On July 11, 1997, the announcement was made in the journal Cell that
> >Neanderthal mitochondrial DNA (mtDNA) had been successfully recovered
> >and sequenced by Svante Pääbo and his team.25
More recent information is available from much of the same crew
at
http://www.eva.mpg.de/genetics/evgen/Krings_DNAseqProc1999.pdf
Haven't read the old one, but I believe the new one is much
of the same stuff with more detail.
[snip]
> >
> >If mtDNA was in fact isolated from the Neanderthal bones, these
> >conclusions might seem reasonable until one considers a few more
> >facts. The Cell article itself noted that the range of sequence
> >differences for modern human mtDNA goes from 1 to 24 with an average
> >of 8 substitutions. The mtDNA sequence differences between modern
> >humans and the single Neanderthal fossil range from 22 to 36
> >substitutions, with the average being 27. In other words, the two
> >most different humans analyzed in this study, as far as mtDNA
> >substitutions are concerned, are different by 24 substitutions. The
> >closest that any human in this study was to the single specimen of
> >Neanderthal mtDNA was 22 substitutions.
I want to plagiarize this later
> > This means that there are
> >some people living today that are closer to Neanderthals in their
> >mtDNA sequencing than they are to some other modern human beings.
> >Someone might be found to be only 22 substitutions away from our
> >Neanderthal, but 24 substitutions away from his own next-door
> >neighbor. Interesting isn't it? If Neanderthals are classed as
> >separate species because of these differences, which one of our modern
> >human volunteers should be classify as a separate species? Perhaps
> >the one who had only 22 substitutions different from the Neanderthal?
> >Or, maybe his neighbor who had 24 substitutions away from him?
>
> chances are that my neighbor has Neanderthal mtDNA -- or maybe I do.
> Seems like what this is boiling down to is that they found the bones
> of a homo sapien and called it by a new name, "Neanderthal."
You may want to have a peak at
http://www.eva.mpg.de/genetics/evgen/Krings_DNAseqProc1999.pdf
Something that Dr. Pittman isn't telling you is that the lower
range of bonobos/chimp - human differences fell inside the extreme
ranges for the bonobos/chimps. The lower end for human - chimp/bonobo
differences was 78, the extreme for chimps/bonobos was 81.
His argument doesn't hold.
Taking his statement:
"This means that there are
some people living today that are closer to Neanderthals in their
mtDNA sequencing than they are to some other modern human beings."
By borrowing his habit of cherry picking convenient data from the
quoted study I can get it to read:
"This means that there are
some bonobos/chimps living today that are closer to humans in their
mtDNA sequencing that they are to some other bonobos/chimps."
[snip]
>
> hallooo, Adam -- I vote for this as POTM.
>
Did you not notice that he spent half of the post casting
doubt on the feasability of Neanderthal MtDNA sequencing
and the other half selectively harvesting data from
Neanderthal MtDNA studies to support his "ideas"?
Harlequin
news:3DBB0450...@crosswinds.net:
[snip -- what "Sean Pitman M.D." wrote]
> Did you actually read the paper this purported "quote" is from? (Krings
> et al. 1997. Neandertal DNA sequences and the origin of modern humans.
> Cell, 90:19-30) You've taken three different paragraphs from pages
> 24-25, 25, and 27 and strung them all together. But these quotes are all
> available on this page at Answers In Genesis:
> http://www.answersingenesis.org/docs/4218tj_v12n1.asp
>
> In fact, a lot of the material you use in this post is available on that
> page.
gen2rev, nice catch. Pitman also has the same quotes at
http://naturalselection.0catch.com/Files/Early%20Man.html
citing the _Cell_ paper without any indication that it is a secondary
citation.
Dr. Pitman, I really should not have to tell you that if you
cite something in a footnote, it is an outright claim that
you have actually checked that source. If you
have to use a quote from a source you have not personally examined
than you MUST add a "quoted by" (or an equivalent) to your
references to indicate that the quote is from a secondary source.
Dunno
On Sat, 26 Oct 2002, zoe_althrop wrote:
In 1997 379 base pairs were recovered, 340 in 1999 out of about
16000. MtDNA is a bit easier to recover than nuclear because
there are between 500 and 1000 copies in cells.
http://www.talkorigins.org/faqs/homs/mtDNA.html
If I recollect from earlier postings on this forum, the MtDNA
was recovered from teeth, which is much more durable than
teeth or even bone which gives extra opportunity.
> >
> >This is just another one of your crappy views of reality.
>
> impressive response here.
>
> >I don't have
> >time to tell you where you are obviously wrong,
>
> too bad. I might have learned something from you, too, from another
> perspective. So far Dr. Sean is ahead.
You may learn something from this
http://www.eva.mpg.de/genetics/evgen/Krings_DNAseqProc1999.pdf
Before attacking Pokemoto with too much vitriol, you
may want to chew on the table below obtained from
testing the sequences obtained in 1999. It's more
than obvious that using the MtDNA sequences recovered
to ascertain what he is trying to wrt humans and
Neanderthals is really stretching it. While it is true
that the most extreme human difference (35) is more
than the least extreme human - neandertal difference (29),
it is also true that the most extreme chimp/bonobo
difference (81) is more than the least extreme human -
chimp/bonobo difference (78).
So, the neanderthal lies within the extreme
variations of humans, but we also have humans that
lie within the extreme variations of the chimps/bonobos.
The neanderthal vs chimp/bonobo is outside of the
extreme variations of the chimp/bonobos.
You don't have to be a biologist (I'm not) to ascertain
that what Dr. Pitman is attempting to deduce with the
available data is absurd.
-------------------------------------------------------------
| Pairwise | Human Neandertal Chimpanzees |
| Differences | and Bonobos |
|---------------+-------------------------------------------|
| | |
|Human (663) | 10.9 +- 5.1 35.3 +- 2.3 93.4 +- 7.1 |
| | (1-35) (29-43) (78-113) |
| | |
|Neandertal (1) | 94.1 +- 5.7 |
| | (84-103) |
| | |
|Chimpanzee (9) | 54.8 +- 24 |
|and Bonobos | (1-81) |
-------------------------------------------------------------
(borrowed chart from a Chris Ho-Stuart post, but checked the numbers
with the article)
>
> > but you have wasted quite
> >a bit of time for no reason.
>
> not at all. I have learned a lot from him already.
So have I. I have learned that he could've have used a more
recent study with more detail, but didn't. The more recent
study (the link I provided) has data that ruins his premise.
>
> > Just read the papers on Neandertal DNA.
> >You can't find a single one that claims to get DNA from 120,000 year old
> >Neandertal fossils. What you do find is that bones from warmer climates
> >no matter what their age are less useful to these analysis than the bones
> >from Europe. Conditions have a lot to do with preservation.
> >
> >You seem to miss the point of the analysis. How you can claim that
> >certain Neandertal sequences are closer to modern humans using your
> >method is beyond good sense and reason. Find out how these analyses are
> >really done. All Neandertal mitochondrial sequences
>
> ALL? All five or six of them?
If you think there are too few samples to be informative, why are
you so quick to champion a single data point in the analysis as
proof that Neanderthals and modern humans are one in the same?
[snip Pokemoto attack]
Sean Pitman M.D.
> >chances are that my neighbor has Neanderthal mtDNA -- or maybe I do.
> >Seems like what this is boiling down to is that they found the bones
> >of a homo sapien and called it by a new name, "Neanderthal."
>
> Please present supporting data.
http://naturalselection.0catch.com/Files/Early%20Man.html
The supporting data is the fact that some humans living today are
closer in their mtDNA sequencing (for the variable region in question)
to Neanderthal sequencing than they are to the sequences of other
humans living today. For example, a human might be off by only 22
substitutions from a Neanderthal, but when compared to his next-door
neighbor, he/she might be different by 24 substitutions. This
next-door neighbor might also be different from the Neanderthal
sequence by say... 24 substitutions. Which one of the three is
therefore a separate species?
A common argument given to explain how Neanderthals are separate
species, at least one given on T.O., is to say that if the average
height for a human was 5 feet, and the range for human height was 3.5
feet to 7 feet (a range of 3.5 feet), finding a skeleton that is 9
feet tall would clearly fall outside this range of what is possible
for the human species to achieve. Arguing that the difference between
7 feet and 9 feet (a difference of 2 feet) is less than the difference
that exists in the normal human range (3.5 feet) does not mean that
the 9-foot specimen can be included in the human range.
Let me ask you... who says? It's not so hard for me to imagine how
this could happen. For example, lets suppose that a nuclear holocaust
wiped out the entire human race except for a small tribe of pigmies.
This pigmy tribe reproduced and grew over the course of several
hundred years. But they are still short. Their range for height is
between 3 and 5 feet. One day they discover the remains of Shaquille
O'Neal, a 7 foot one inch 315 pound giant. Clearly he is out of the
range of these pigmy survivors... and thus clearly he belongs to
different species. Wouldn't they be surprised to know that he in fact
came from their very own species?
The same might easily be true of our relation to Neanderthals. The
clustering average of Neanderthal mtDNA substitutions does appear to
be quite distinct from the clustering average of modern humans.
However, taking modern humans, it would be possible to isolate groups
that have a wider sequence variation than exists between some humans
and Neanderthals. Once isolated, these groups could produce an
isolated population that would cluster around these widely separated
mtDNA substitution "averages". One human cluster average (ethnic
average) might be 24 substitutions different from another human
cluster average. Then, this second human cluster might be only 22
substitutions away from the Neanderthal cluster average. Which
cluster then is the new species? Ethnic groups are formed because of
isolation. They develop unique clusters of features as well as
genetic anomalies. Does this mean that they are different species
just because they are separated from other ethnic groups by a certain
number of genetic substitutions in a mtDNA variable region? I think
that this assumption... assumes too much.
Sean
zoe_althrop
wrote:
snip>
zoe wrote:
>>Ron must have many bad days, then. I've seen this kind of response
>>from him before...a curmudgeon, if I ever saw one.
>
>Zoe, you are just showing yourself to be in outer space somewhere. Think back,
>I'm the one that tried to patiently correct your misconceptions. I have even
>defended your feeble attempts when you first came here, and it seemed like you
>had some honest questions. You can probably do a Google search from those
>early days and see that I was one of the guys that came out against the first
>brutal lashings that you were given because I thought that they were being
>unfair. I have never called the junk that you come up with "crappy" as far as
>I can recall. I just gave up trying to educate you a very long time ago.
forgive me, Ron, you are correct. I googled back and discovered that
you have, for the most part, conducted your communications in a very
civil manner, at least with me.
Truth is, though, I consider most regulars on here to be curmudgeons.
I guess what I should have said was that your post to Dr. Pitman was a
curmudgeon-type post, if I ever saw one. Anyway, please accept my
sincere apologies for mis-casting you.
>I
>only castigate the people that I think should know better. This group never
>included you.
<grin> -- I guess that's a compliment to Sean Pitman, while I have
managed to escape due to my lowly student status.
snip>
>>>It's a pity that you only choose to learn from teachers of dubious quality.
>>
>>please note that my learning is as a result of scientific data,
>>thoughtfully discussed. I think I can judge the quality of my
>>teachers for myself, thank you.
>
>Obviously you are mistaken if you can't see what is wrong with what Sean is
>dishing out.
then it would have helped if you had addressed his "errors", since, so
far, what he says is quite enlightening to me, and I don't see the
errors you say you see.
>Why is it that you think that what Sean writes is OK, but nothing anyone writes
>correcting your misconceptions about isochrons seems to register with you?
I don't know what you mean. I think Jon Fleming is a great teacher,
and so would Bjoern be if he weren't so cantankerous. Eric Rowley is
good, too, as is Drearash. I've learned a lot from these guys. The
only problem they have with me, I guess, is that I take my learning
and do with it as I please when it comes to final conclusions.
>>>>> Just read the papers on Neandertal DNA.
>>>>>You can't find a single one that claims to get DNA from 120,000 year old
>>>>>Neandertal fossils. What you do find is that bones from warmer climates
>>>>>no matter what their age are less useful to these analysis than the bones
>>>>>from Europe. Conditions have a lot to do with preservation.
>>>>>
>>>>>You seem to miss the point of the analysis. How you can claim that
>>>>>certain Neandertal sequences are closer to modern humans using your
>>>>>method is beyond good sense and reason. Find out how these analyses are
>>>>>really done. All Neandertal mitochondrial sequences
>>>>
>>>> ALL? All five or six of them?
>>>
>>>Yes.
>>
>>that's not good enough, and you know it, Mark.
>
>What any sane person would realize is that just one Neandertal sequence that
>falls well outside of the variation found in extant humans is a very large
>problem for people like yourself that think that everyone was created just a
>few thousand years ago.
that would be a problem, yes, if the perspective is one of needing
millions of years to evolve. But humans can vary in their sequences
over a short period of time if they have been programmed to vary from
the beginning. No need for all that time.
>Are Neandertals human?
I would guess yes -- a different species of human, but still human. I
mean, just recently, I saw a taxi driver, a living, breathing human
taxi driver, whose cranium was shaped like some of those early
drawings of ancient hominids -- the brow projected far out above the
eyes, hung low, and sloped back, with very little forehead in
evidence. If he were to die and be found a few years from now, he
would probably be considered some kind of missing link. Yet there he
was, driving a car and acting like any other normal human being.
>Are they some other creation?
probably a result of inbreeding so that certain features and
characteristics became more pronounced.
>Why aren't they mentioned in the Bible?
the Bible is written for other purposes than science, but it does
mention that there were giants in those days, some called Nephilim,
others Rephaim, and so on.
snip>
>>>We do have pretty good ideas as to the limits of variability in modern
>>>humans.
>>
>>where did these ideas come from? Which eyewitnesses? Can they be
>>trusted?
>
>We have sequences for thousands of humans from all the different continents.
>It is a fact that the Neandertal sequences fall outside of the variation that
>we have observed. No, we probably never will have the DNA sequences for the
>billions of people that currently exist, but if you are willing to fund such a
>study I'm sure that you will find a group of researchers that would be willing
>to sequence much larger sample sizes.
how much does it take to finance such a quest? Let me check my
piggybank.
>How do you think that you cross check for contamination? My wife worked in a
>lab where they were sequencing a lot of human D-loop sequences looking into the
>origins of native Americans. They all knew what haplotype they were. I'm sure
>that the people doing the Neandertal work know that they do not have Neandertal
>type mitochondrial DNA to contaminate the samples with.
did they know the haplotypes of the workers who helped dig up these
bones?
>You could do this research yourself if you don't trust the people doing it.
>You don't have to have any evolutionary conceptions to just go out and find out
>what exists out there. Do you think that the automated DNA sequencers are
>biased and only give the results that we want?
no, but four or five samples are insufficient when the comparison is
being made to billions of humans. I mean, if a few million
Neanderthal sequences had been obtained, then you would have more of
an ability to tell if they all fell outside human sequences or if many
crossed over.
>>> All existing Neanderthal sequences fall outside those limits.
>>
>>all four or five of them, right. I'm impressed by your
>>four-person-high mountains of evidence.
>
>Considering the evidence that you have, it is a mountain, isn't it?
the evidence I have is the same evidence you have, except that you
have chosen to draw what I would consider to be premature conclusions,
and I have chosen to leave the door wide open.
>Explain
>the evidence that we have. Why complain that we don't have enough if it is
>enough to say that you are full of baloney. Give an explanation for the
>Neandertal sequences that is consistent with your model. If you can't explain
>a couple of sequences, what makes you think that you could explain 10 or a
>hundred?
10 or 100 would just barely begin to allow some general pattern to
form.
>Why do you think that you have a chance of coming up with something
>that would negate the results when they come from different countries and from
>fossils from different time periods?
I don't understand your question. Besides, I am not trying to negate
any results in this thread. I just mentioned that I thought the post
was excellent.
snip>
>No, Pitman isn't a peer of mine. You know this as well as I do.
no, I don't. I don't know your educational background, and figured
that you were at least as educated as he appears to be. Not that it
matters to me, the education, as long as the ideas are sound.
>He is just a
>well educated person that would rather use his intellect to obfuscate the
>issues instead of trying to learn something about nature. You would probably
>know why he does this better than I would.
grrrr...you're being a curmudgeon now.
----
zoe
zoe_althrop
<wett...@attbi.com> wrote:
snip>
>As amusing as the your endless lack of comprehension about isochrons have
>been, they have not illustrated any ability for you to comprehend anything.
that would be better phrased: "they have not illustrated any ability
for you to comprehend our point of view."
Or you mine.
snip>
>>>>>You seem to miss the point of the analysis. How you can claim that
>>>>>certain Neandertal sequences are closer to modern humans using your
>>>>>method is beyond good sense and reason. Find out how these analyses are
>>>>>really done. All Neandertal mitochondrial sequences
>>>>
>>>> ALL? All five or six of them?
>>>
>>>Yes.
>>
>> that's not good enough, and you know it, Mark.
>
>All available ones fall outside. All of them.
that does not necessarily prove anything. What if, in a large enough
sampling universe, the sequences covered the whole spectrum from
outside to inside? A mere four or five might just happen to be from
that part of the spectrum that falls outside.
> When we have more of them,
>there might be something else to discuss.
right. Until then, conclusions should not be prematurely drawn.
snip>
>> where did these ideas come from? Which eyewitnesses? Can they be
>> trusted?
>
>Science doesn't rely on eyewitness testimony Zoe.
it had better rely on something observed. What else is eyewitness
testimony but first-person observation of the data?
snip>
----
zoe
zoe_althrop
This makes absolute sense to me. I'm sure Jon will acknowledge this
to be reasonable...right, Jon?
----
zoe
zoe_althrop
<muen...@hushmail.com> wrote:
snip>
>In 1997 379 base pairs were recovered, 340 in 1999 out of about
>16000. MtDNA is a bit easier to recover than nuclear because
>there are between 500 and 1000 copies in cells.
>
>http://www.talkorigins.org/faqs/homs/mtDNA.html
>
>If I recollect from earlier postings on this forum, the MtDNA
>was recovered from teeth, which is much more durable than
>teeth or even bone which gives extra opportunity.
MtDna is more durable than teeth? How so?
snip>
>You may learn something from this
>http://www.eva.mpg.de/genetics/evgen/Krings_DNAseqProc1999.pdf
>
>Before attacking Pokemoto with too much vitriol, you
>may want to chew on the table below obtained from
>testing the sequences obtained in 1999. It's more
>than obvious that using the MtDNA sequences recovered
>to ascertain what he is trying to wrt humans and
>Neanderthals is really stretching it. While it is true
>that the most extreme human difference (35) is more
>than the least extreme human - neandertal difference (29),
>it is also true that the most extreme chimp/bonobo
>difference (81) is more than the least extreme human -
>chimp/bonobo difference (78).
personally, I don't see what such comparisons really say about
origins, per se. I mean, why don't you put the mouse in there and see
what you get. After a while, there is no particular rhyme or reason
that points to a common ancestor. The best you would do is determine,
as Sean is doing, that it is premature to consider Neanderthals to be
a species separate from humans.
>
>So, the neanderthal lies within the extreme
>variations of humans, but we also have humans that
>lie within the extreme variations of the chimps/bonobos.
>The neanderthal vs chimp/bonobo is outside of the
>extreme variations of the chimp/bonobos.
>
>You don't have to be a biologist (I'm not) to ascertain
>that what Dr. Pitman is attempting to deduce with the
>available data is absurd.
His deduction, as far as I could tell, was simply that there is
insufficient information to come to the conclusions that evolutionsts
have prematurely arrived at.
>
>
>-------------------------------------------------------------
>| Pairwise | Human Neandertal Chimpanzees |
>| Differences | and Bonobos |
>|---------------+-------------------------------------------|
>| | |
>|Human (663) | 10.9 +- 5.1 35.3 +- 2.3 93.4 +- 7.1 |
>| | (1-35) (29-43) (78-113) |
>| | |
>|Neandertal (1) | 94.1 +- 5.7 |
>| | (84-103) |
>| | |
>|Chimpanzee (9) | 54.8 +- 24 |
>|and Bonobos | (1-81) |
>-------------------------------------------------------------
>(borrowed chart from a Chris Ho-Stuart post, but checked the numbers
>with the article)
and from this you gather what?
>
>
>>
>> > but you have wasted quite
>> >a bit of time for no reason.
>>
>> not at all. I have learned a lot from him already.
>
>So have I. I have learned that he could've have used a more
>recent study with more detail, but didn't. The more recent
>study (the link I provided) has data that ruins his premise.
maybe you might want to restate his premise to be sure you are not
attacking a strawman premise?
>> > Just read the papers on Neandertal DNA.
>> >You can't find a single one that claims to get DNA from 120,000 year old
>> >Neandertal fossils. What you do find is that bones from warmer climates
>> >no matter what their age are less useful to these analysis than the bones
>> >from Europe. Conditions have a lot to do with preservation.
>> >
>> >You seem to miss the point of the analysis. How you can claim that
>> >certain Neandertal sequences are closer to modern humans using your
>> >method is beyond good sense and reason. Find out how these analyses are
>> >really done. All Neandertal mitochondrial sequences
>>
>> ALL? All five or six of them?
>
>If you think there are too few samples to be informative, why are
>you so quick to champion a single data point in the analysis as
>proof that Neanderthals and modern humans are one in the same?
did I say anything about proof? I think the bottom line here is that
there is insufficient information to form even a premature conclusion
that Neanderthals are a different species.
----
zoe
zoe_althrop
<muen...@hushmail.com> wrote:
snip>
>Did you not notice that he spent half of the post casting
>doubt on the feasability of Neanderthal MtDNA sequencing
>and the other half selectively harvesting data from
>Neanderthal MtDNA studies to support his "ideas"?
the impression I gathered was that he thought the feasibility of the
sequencing was very much in doubt to start with, but IF you are going
to accept it, then here are some further problems.....
----
zoe
Sean Pitman M.D.
> This is just another one of your crappy views of reality. I don't have
> time to tell you where you are obviously wrong, but you have wasted quite
> a bit of time for no reason.
Even from your perspective, I fail to see how I have "wasted time." I
can be used by you as a clear example of how those who don't see
things according to an evolutionary viewpoint are "nuts." Your
comebacks to my feeble mutterings can be used as examples of how to
answer the crazy thoughts and claims of illogical
anti-evolutionists/design theorists/creationists. So, your time is
not wasted even if I am personally incapable of understanding your
brilliance, because others will certainly recognize it for what it is.
> Just read the papers on Neandertal DNA.
I have read quite a few actually.
> You can't find a single one that claims to get DNA from 120,000 year old
> Neandertal fossils.
Yes, that is true. The claims are that mtDNA was obtained from
Neanderthal bones ranging in ages from 30,000 to 50,000 years.
However, the reason I comment on DNA decay rates is because claims for
the isolation of DNA dating millions of years has also been made (ie.
from insects in amber). The relatively rapid DNA decay rates also
limit the number of Neanderthal specimens that DNA can be successfully
isolated from... significantly. From what I have read, only three
Neanderthals have been found to have DNA that is preserved well enough
to sequence. It seems like environmental conditions have to be just
right or the relatively fragile DNA won't last even a few thousand
years, much less tens of thousands of years.
> What you do find is that bones from warmer climates
> no matter what their age are less useful to these analysis than the bones
> from Europe. Conditions have a lot to do with preservation.
Oh, I agree...
> You seem to miss the point of the analysis. How you can claim that
> certain Neandertal sequences are closer to modern humans using your
> method is beyond good sense and reason. Find out how these analyses are
> really done. All Neandertal mitochondrial sequences fall outside the
> range of modern humans, but they do group with each other.
Yes, I am aware of this. All Neandertals (all three of them) fall
outside the statistical range for modern human mtDNA substitutions for
the variable region in question. I thought I made this fact perfectly
clear in my discussion. The three Neanderthals also group with each
other, as humans group with each other. My point is that there exist
living humans that are closer to the Neanderthal sequence than they
are to other living humans. In other words, a given person might be
only 22 substitutions different from a Neanderthal while that same
person is 24 substitutions different from his own next-door neighbor.
Given these three individuals alone, which one belongs to a different
species?
> This just
> means that all Neandertals that have been sequenced are more closely
> related to each other than they are to any extant human.
Yes, they are. But ethnic clustering also occurs and can
theoretically occur between ethnic groups that are more different in
the number of mtDNA substitutions than some groups are different from
Neanderthal mtDNA. Given such wide ranges of possible substitution
differences, how can one determine which ethnic group should be
classed as a separate species?
> They are
> related to us, they fall between modern humans and chimps.
Actually, Neanderthals do not fall between modern humans and chimps.
Check your references. Neanderthals actually fall farther away from
chimps than humans do as far as substitution differences. From the
"modern human" perspective, there are fewer differences, on average,
between us and Neanderthals than there are between us and chimps.
Likewise, from the Neanderthal's perspective, there are also fewer
differences between Neanderthal's and humans than between Neanderthals
and chimps. It gets interesting however when you look at it from the
chimp's perspective. From the chimp's perspective, there are fewer
differences between chimps and modern humans than there are between
chimps and Neanderthals. Using this logic, it is the modern human
that is more closely related to the chimps than Neanderthals are.
> What a waste
> of a brain. You seemed to have some promise in the beginning, but you
> are becoming lamer as time goes on. You must realize at some level that
> the reason for this is because your position is so weak that trying to
> support it with propaganda tracts like these makes you look pretty
> stupid.
Stupid is as stupid does...
I ain't a smart man, but I has been lucky enough to makes it thru
medicul skool. Good or bad, rite or wrong, smart or dum, I is trewly
beleevin whats I is sayin. I thanks you thow for sharin your hi
minded thawts with me. Perhaps tho, I jus am incapable of
understandin such wonders as you do seems to know so well. Someday I
juz hopes to be a smart as you is.
> Ron Okimoto
Sean ; )
Adam Marczyk
news:fd67d42a.02102...@posting.google.com...
I think all you've shown is that the boundaries between species are often very
fuzzy things. I also think the determination that Neanderthals are a separate
species was made on the basis of morphology, not on genetics. Morphologically
they're quite distinct from us; genetically they may have been (almost certainly
were) very similar to us. In much the same way, lions and tigers are very
closely related - we even know they can interbreed, it's been done - but they're
undoubtedly distinct species in their own right.
--
And I want to conquer the world,
give all the idiots a brand new religion,
put an end to poverty, uncleanliness and toil,
promote equality in all of my decisions...
--Bad Religion, "I Want to Conquer the World"
http://www.ebonmusings.org ICQ: 8777843 PGP Key ID: 0x5C66F737
zoe_althrop
if this is all true, then I think evolutionists should go back to the
drawing board.
----
zoe
Dunno
On Sun, 27 Oct 2002, zoe_althrop wrote:
>
>
> On Sun, 27 Oct 2002 00:22:15 +0000 (UTC), Dunno
> <muen...@hushmail.com> wrote:
>
> snip>
>
> >In 1997 379 base pairs were recovered, 340 in 1999 out of about
> >16000. MtDNA is a bit easier to recover than nuclear because
> >there are between 500 and 1000 copies in cells.
> >
> >http://www.talkorigins.org/faqs/homs/mtDNA.html
> >
> >If I recollect from earlier postings on this forum, the MtDNA
> >was recovered from teeth, which is much more durable than
> >teeth or even bone which gives extra opportunity.
>
> MtDna is more durable than teeth? How so?
A little fat fingering on the keyboard, I was trying to
watch tv while composing a post. What I was trying to
say was that teeth are more durable than soft tissue
or even bone, thus affording extra opportunity to
extract MtDNA. The "soft tissue" part got lost between
brain and keyboard and was likely typed into my
tv remote.
[snip]
> >
> >-------------------------------------------------------------
> >| Pairwise | Human Neandertal Chimpanzees |
> >| Differences | and Bonobos |
> >|---------------+-------------------------------------------|
> >| | |
> >|Human (663) | 10.9 +- 5.1 35.3 +- 2.3 93.4 +- 7.1 |
> >| | (1-35) (29-43) (78-113) |
> >| | |
> >|Neandertal (1) | 94.1 +- 5.7 |
> >| | (84-103) |
> >| | |
> >|Chimpanzee (9) | 54.8 +- 24 |
> >|and Bonobos | (1-81) |
> >-------------------------------------------------------------
> >(borrowed chart from a Chris Ho-Stuart post, but checked the numbers
> >with the article)
>
> and from this you gather what?
>
Most likely that Dr. Pitman didn't peruse the more recent article
before posting.
Harlequin
news:fd67d42a.0210...@posting.google.com:
[snip]
>> They are
>> related to us, they fall between modern humans and chimps.
>
> Actually, Neanderthals do not fall between modern humans and chimps.
> Check your references. Neanderthals actually fall farther away from
> chimps than humans do as far as substitution differences. From the
> "modern human" perspective, there are fewer differences, on average,
> between us and Neanderthals than there are between us and chimps.
> Likewise, from the Neanderthal's perspective, there are also fewer
> differences between Neanderthal's and humans than between Neanderthals
> and chimps. It gets interesting however when you look at it from the
> chimp's perspective. From the chimp's perspective, there are fewer
> differences between chimps and modern humans than there are between
> chimps and Neanderthals. Using this logic, it is the modern human
> that is more closely related to the chimps than Neanderthals are.
[snip]
Fewer differences between chimps and modern humans than between chimps
and neandertals? One would expectthat that these should be
about the same. Let us look at the data. It has already
been presented in other post so I will copy and paste it.
-------------------------------------------------------------
| Pairwise | Human Neandertal Chimpanzees |
| Differences | and Bonobos |
|---------------+-------------------------------------------|
| | |
|Human (663) | 10.9 +- 5.1 35.3 +- 2.3 93.4 +- 7.1 |
| | (1-35) (29-43) (78-113) |
| | |
|Neandertal (1) | 94.1 +- 5.7 |
| | (84-103) |
| | |
|Chimpanzee (9) | 54.8 +- 24 |
|and Bonobos | (1-81) |
-------------------------------------------------------------
The data comes from an article which can be accessed at
http://www.pnas.org/cgi/content/full/96/10/5581
(This is a different URL for it than was given by the other
posts. This version is a bit more useful. And I have verified
that the data was copied correctly.)
I would say that is a VERY good fit to the evolutionary
expectations.
Pokemoto
>Path:
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>From: muz...@aol.com (zoe_althrop)
>Newsgroups: talk.origins
>Date: Sun, 27 Oct 2002 02:28:15 +0000 (UTC)
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I'm sorry Zoe, but it isn't your student status. I just think that you truely
believe the things that you do and are mentally incapable of putting two
concepts together that would run counter to those beliefs.
>
>snip>
>
>>>>It's a pity that you only choose to learn from teachers of dubious
>quality.
>>>
>>>please note that my learning is as a result of scientific data,
>>>thoughtfully discussed. I think I can judge the quality of my
>>>teachers for myself, thank you.
>>
>>Obviously you are mistaken if you can't see what is wrong with what Sean is
>>dishing out.
>
>then it would have helped if you had addressed his "errors", since, so
>far, what he says is quite enlightening to me, and I don't see the
>errors you say you see.
It really isn't worth my time. Pitman knows what he is doing is bogus. You
would know it too if you could just let yourself see it.
>
>>Why is it that you think that what Sean writes is OK, but nothing anyone
>writes
>>correcting your misconceptions about isochrons seems to register with you?
>
>I don't know what you mean. I think Jon Fleming is a great teacher,
>and so would Bjoern be if he weren't so cantankerous. Eric Rowley is
>good, too, as is Drearash. I've learned a lot from these guys. The
>only problem they have with me, I guess, is that I take my learning
>and do with it as I please when it comes to final conclusions.
They may be very good teachers, but you haven't let yourself learn very much
have you? Can you see why even the guys at the ICR think that Isochron is a
big problem for them and that they really have no good argument against it?
They can only resort to what you try and do, and claim that things are that way
for some unknown reason or just by chance. How reasonable is it that all of
these rocks have just the right amounts of parent and decay products just by
chance, and that some rocks can be cross dated using different isotopes?
>
>>>>>> Just read the papers on Neandertal DNA.
>>>>>>You can't find a single one that claims to get DNA from 120,000 year old
>>>>>>Neandertal fossils. What you do find is that bones from warmer climates
>>>>>>no matter what their age are less useful to these analysis than the
>bones
>>>>>>from Europe. Conditions have a lot to do with preservation.
>>>>>>
>>>>>>You seem to miss the point of the analysis. How you can claim that
>>>>>>certain Neandertal sequences are closer to modern humans using your
>>>>>>method is beyond good sense and reason. Find out how these analyses are
>>>>>>really done. All Neandertal mitochondrial sequences
>>>>>
>>>>> ALL? All five or six of them?
>>>>
>>>>Yes.
>>>
>>>that's not good enough, and you know it, Mark.
>>
>>What any sane person would realize is that just one Neandertal sequence that
>>falls well outside of the variation found in extant humans is a very large
>>problem for people like yourself that think that everyone was created just a
>>few thousand years ago.
>
>that would be a problem, yes, if the perspective is one of needing
>millions of years to evolve. But humans can vary in their sequences
>over a short period of time if they have been programmed to vary from
>the beginning. No need for all that time.
If you had some evidence to back up this assertion you might have something,
but since you don't it is a worthless assertion.
>
>>Are Neandertals human?
>
>I would guess yes -- a different species of human, but still human. I
>mean, just recently, I saw a taxi driver, a living, breathing human
>taxi driver, whose cranium was shaped like some of those early
>drawings of ancient hominids -- the brow projected far out above the
>eyes, hung low, and sloped back, with very little forehead in
>evidence. If he were to die and be found a few years from now, he
>would probably be considered some kind of missing link. Yet there he
>was, driving a car and acting like any other normal human being.
You have some weird concept of sampling error. What type of modern human is
the most likely to fossilize today? Wouldn't you expect the most common type
to be the most common type to also fossilize. This would be the same today as
it would be thousands of years ago. Why can all Neandertals be grouped
together whether they are found in the middle east or Europe? These aren't
just funny looking modern humans or we would find modern humans mixed in with
them.
>
>>Are they some other creation?
>
>probably a result of inbreeding so that certain features and
>characteristics became more pronounced.
I assume that your evidence for this is with your evidence for your other
assertions of similar value.
>
>>Why aren't they mentioned in the Bible?
>
>the Bible is written for other purposes than science, but it does
>mention that there were giants in those days, some called Nephilim,
>others Rephaim, and so on.
You have a pretty low opinion of the gods of the Bible if you think that
Neandertals are the half gods.
>
>snip>
>
>>>>We do have pretty good ideas as to the limits of variability in modern
>>>>humans.
>>>
>>>where did these ideas come from? Which eyewitnesses? Can they be
>>>trusted?
>>
>>We have sequences for thousands of humans from all the different continents.
>
>>It is a fact that the Neandertal sequences fall outside of the variation
>that
>>we have observed. No, we probably never will have the DNA sequences for the
>>billions of people that currently exist, but if you are willing to fund such
>a
>>study I'm sure that you will find a group of researchers that would be
>willing
>>to sequence much larger sample sizes.
>
>how much does it take to finance such a quest? Let me check my
>piggybank.
About 40 dollars a sample would do it, but it used to cost more when most of
the work was actually done. This assumes that collecting the samples doesn't
cost a whole lot.
>
>>How do you think that you cross check for contamination? My wife worked in
>a
>>lab where they were sequencing a lot of human D-loop sequences looking into
>the
>>origins of native Americans. They all knew what haplotype they were. I'm
>sure
>>that the people doing the Neandertal work know that they do not have
>Neandertal
>>type mitochondrial DNA to contaminate the samples with.
>
>did they know the haplotypes of the workers who helped dig up these
>bones?
Zoe you keep making this blunder and you don't even realize what you are doing.
We have sufficiently sampled the extant human race to know that it is unlikely
that we will find Neandertal like samples in any extant human. I'd like to
find some, it wouldn't bother me a bit. We share some of our MHC alleles with
chimps. Some of the variation in our genomes is very ancient. There is no law
that says that we can't maintain such variation by just dumb luck or by
selection. If our ancestors had this variation we could have this variation.
It is that thing called common descent.
If Neandertal sequences exist in the current population they would have to be
very rare. It is very unlikely that the people that found and preped the bones
all had someone with Neandertal DNA in the group. One group is a possibility,
but all the research groups is not at all very likely. Neandertal like
sequences probably do not exist in the current human population.
If contamination were a problem why would only the Neandertal like sequences be
recovered?
>
>>You could do this research yourself if you don't trust the people doing it.
>>You don't have to have any evolutionary conceptions to just go out and find
>out
>>what exists out there. Do you think that the automated DNA sequencers are
>>biased and only give the results that we want?
>
>no, but four or five samples are insufficient when the comparison is
>being made to billions of humans. I mean, if a few million
>Neanderthal sequences had been obtained, then you would have more of
>an ability to tell if they all fell outside human sequences or if many
>crossed over.
Zoe, you don't need millions of Neandertal sequences and you know it. Just two
from different locations and you have a pretty good idea. Three is better,
etc. Why would only the Neandertal sequences that fall outside of the range of
modern humans be the ones that are found? Why can't you go out and pick three
different living humans at random and find at least one Neandertal like
sequence? I haven't kept up with the research, but I'd bet the number of
extant human sequences number in the tens of thousand without finding a single
sequence like Neandertal, and these researchers have been looking for
diversity. What you seem to be missing is that by sampling just these few
thousand humans they have actually sampled hundreds of millions. If one of
your very distant cousins has been included in the testing and you share some
great, great, great maternal grandmother, you have been sampled too. All of
their extant maternal relatives have also been sampled. They haven't just been
looking at some small inbred population, they have been covering the globe to
get their samples. It is a possibility that we will find other mitochondrial
types, but these types will be rare if they exist.
>
>>>> All existing Neanderthal sequences fall outside those limits.
>>>
>>>all four or five of them, right. I'm impressed by your
>>>four-person-high mountains of evidence.
>>
>>Considering the evidence that you have, it is a mountain, isn't it?
>
>the evidence I have is the same evidence you have, except that you
>have chosen to draw what I would consider to be premature conclusions,
>and I have chosen to leave the door wide open.
You can't evaluate the evidence in a coherant fashion. It is your bias that is
the problem and not mine or any other scientist. I'd like to think that at
some level you realize this, but from your past posts this would seem unlikely.
>
>>Explain
>>the evidence that we have. Why complain that we don't have enough if it is
>>enough to say that you are full of baloney. Give an explanation for the
>>Neandertal sequences that is consistent with your model. If you can't
>explain
>>a couple of sequences, what makes you think that you could explain 10 or a
>>hundred?
>
>10 or 100 would just barely begin to allow some general pattern to
>form.
You have to take all the data into consideration and look at the pattern. If
we just had 10 modern humans and 3 or 4 Neandertals you would have a point, but
you know that this is not the case.
>
>>Why do you think that you have a chance of coming up with something
>>that would negate the results when they come from different countries and
>from
>>fossils from different time periods?
>
>I don't understand your question. Besides, I am not trying to negate
>any results in this thread. I just mentioned that I thought the post
>was excellent.
Most people that have read your posts, realize that your endorsement isn't
worth much.
What is the most excellent part of his Neandertal blather? Nothing that you've
come up with so far seems to be any good.
>
>snip>
>
>>No, Pitman isn't a peer of mine. You know this as well as I do.
>
>no, I don't. I don't know your educational background, and figured
>that you were at least as educated as he appears to be. Not that it
>matters to me, the education, as long as the ideas are sound.
This would be worth something if your track record wasn't so flaky.
>
>>He is just a
>>well educated person that would rather use his intellect to obfuscate the
>>issues instead of trying to learn something about nature. You would
>probably
>>know why he does this better than I would.
>
>grrrr...you're being a curmudgeon now.
>
>----
>zoe
This is just a fact. If that is being a curmudgeon then I'm a curmudgeon.
Pitman knows better. He only does the things that he does to bolster his world
view. He doesn't do it to learn more about the world, in fact his writings
have exactly the opposite effect on anyone that reads them and thinks that they
have some value, such as a person like yourself. This is vile. Pitman
shouldn't have to obfuscate, he shouldn't have to be dishonest with people like
you. You would believe anything that he writes, just as long as his
conclusions matched yours, so why does he write these essays? Why does he fill
them full of crap? He only deceives people like yourself. He certainly
doesn't convince anyone that understands the data that he has something of
interest.
You might be able to get dewy eyed and praise people like this, but I can't.
Ron Okimoto
Pokemoto
>Path:
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ere.is.no.cabal
>From: Sean...@juno.com (Sean Pitman M.D.)
>Newsgroups: talk.origins
>Date: Sun, 27 Oct 2002 02:51:28 +0000 (UTC)
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>
>
>
>Ron Okimoto
>
>> This is just another one of your crappy views of reality. I don't have
>> time to tell you where you are obviously wrong, but you have wasted quite
>> a bit of time for no reason.
>
>Even from your perspective, I fail to see how I have "wasted time." I
>can be used by you as a clear example of how those who don't see
>things according to an evolutionary viewpoint are "nuts." Your
>comebacks to my feeble mutterings can be used as examples of how to
>answer the crazy thoughts and claims of illogical
>anti-evolutionists/design theorists/creationists. So, your time is
>not wasted even if I am personally incapable of understanding your
>brilliance, because others will certainly recognize it for what it is.
I have to disagree, your writing are dishonest and misleading. You only have
to look at responses like Zoe's to figure that out. I've said to Zoe that I
think that what you are doing is vile and I meant it.
>
>> Just read the papers on Neandertal DNA.
>
>I have read quite a few actually.
You may have read them, but you obviously do not understand them.
>
>> You can't find a single one that claims to get DNA from 120,000 year old
>> Neandertal fossils.
>
>Yes, that is true. The claims are that mtDNA was obtained from
>Neanderthal bones ranging in ages from 30,000 to 50,000 years.
>However, the reason I comment on DNA decay rates is because claims for
>the isolation of DNA dating millions of years has also been made (ie.
>from insects in amber). The relatively rapid DNA decay rates also
>limit the number of Neanderthal specimens that DNA can be successfully
>isolated from... significantly. From what I have read, only three
>Neanderthals have been found to have DNA that is preserved well enough
>to sequence. It seems like environmental conditions have to be just
>right or the relatively fragile DNA won't last even a few thousand
>years, much less tens of thousands of years.
So what, you are just admitting to obfuscating the issues.
The decay rates don't matter if we actually find some DNA to sequence does it?
>
>> What you do find is that bones from warmer climates
>> no matter what their age are less useful to these analysis than the bones
>> from Europe. Conditions have a lot to do with preservation.
>
>Oh, I agree...
>
>> You seem to miss the point of the analysis. How you can claim that
>> certain Neandertal sequences are closer to modern humans using your
>> method is beyond good sense and reason. Find out how these analyses are
>> really done. All Neandertal mitochondrial sequences fall outside the
>> range of modern humans, but they do group with each other.
>
>Yes, I am aware of this. All Neandertals (all three of them) fall
>outside the statistical range for modern human mtDNA substitutions for
>the variable region in question. I thought I made this fact perfectly
>clear in my discussion. The three Neanderthals also group with each
>other, as humans group with each other. My point is that there exist
>living humans that are closer to the Neanderthal sequence than they
>are to other living humans. In other words, a given person might be
>only 22 substitutions different from a Neanderthal while that same
>person is 24 substitutions different from his own next-door neighbor.
>Given these three individuals alone, which one belongs to a different
>species?
You keep repeating this, but it is just wrong. There isn't a single human
sequence that is closer to Neandertal than it is to another human. You are
just looking a gross similarity. This is bogus and if you knew anything about
DNA sequence you would know that it is bogus.
Demonstrate that what you claim is true. Find a modern human sequence that is
closer to Neandertal than it is to another extant human. You claim that they
exist, but only by using the wrong measure. Just because sequences differ by
the same number of substitutions doesn't mean that the substitutions are the
same. Even though two modern human sequences can differ by 24 substitutions
they are different substitutions than the 22 that the closest human and
Neandertals differ by. These are three different individual modern humans.
Your interpretation of the data is bogus. Get the sequences and look at them
yourself. None of them will be closer to Neandertal than they are to another
extant human being. If they are 24 substitutions from eachother they will
likely be more than 24 substitutions from Neandertal. Not only that, but the
sequences will nest within modern humans and will not be found to be from the
Neandertal lineage. You do know about common descent and nested similarity,
don't you? You are using a stupidly simple measure of difference and drawing
the incorrect conclusion from it.
>
>> This just
>> means that all Neandertals that have been sequenced are more closely
>> related to each other than they are to any extant human.
>
>Yes, they are. But ethnic clustering also occurs and can
>theoretically occur between ethnic groups that are more different in
>the number of mtDNA substitutions than some groups are different from
>Neanderthal mtDNA. Given such wide ranges of possible substitution
>differences, how can one determine which ethnic group should be
>classed as a separate species?
So what? You are misinterpreting this data. It does not mean what you think
that it does. You are wrong and your analysis is bogus. You obviously do not
understand what you are talking about. We would not class different ethnic
groups as different species. Why would we? The sequences would still nest
within humans and not outside of humans no matter the gross differences between
them. We don't expect equal and constant evolution in all lineages. You
really don't understand how the analysis is done. A sequence derived from one
ancestral sequence will look different from one derived from a different
ancestral sequence. Long branch lengths tend to collapse the branch lengths
and make distantly related sequences more similar than they really are, and
this occurs in the D-loop sequence, but we can still tell that the Neandertal
sequences are derived from a different starting point. How else do you think
that we can tell that the humans sequences derive from one that existed 75,000
to 150,000 years ago and the Neandertal sequences derive from one that existed
half a million years ago?
>
>> They are
>> related to us, they fall between modern humans and chimps.
>
>Actually, Neanderthals do not fall between modern humans and chimps.
>Check your references. Neanderthals actually fall farther away from
>chimps than humans do as far as substitution differences. From the
>"modern human" perspective, there are fewer differences, on average,
>between us and Neanderthals than there are between us and chimps.
Idiot. This is beneath even you. If the sequences fell where you say, why
would modern humans be 500,000 years distant from the Neandertal type common
ancestor and 5-8 million from the chimp human ancestor.
By anyones measure this is between modern humans (75,000 to 150,000) and
chimps.
>Likewise, from the Neanderthal's perspective, there are also fewer
>differences between Neanderthal's and humans than between Neanderthals
>and chimps. It gets interesting however when you look at it from the
>chimp's perspective. From the chimp's perspective, there are fewer
>differences between chimps and modern humans than there are between
>chimps and Neanderthals. Using this logic, it is the modern human
>that is more closely related to the chimps than Neanderthals are.
What a waste of a brain. You must realize your error by now. Just think about
it for 5 minutes. You are wrong about this, and I can't understand how you
could be this wrong.
>
>> What a waste
>> of a brain. You seemed to have some promise in the beginning, but you
>> are becoming lamer as time goes on. You must realize at some level that
>> the reason for this is because your position is so weak that trying to
>> support it with propaganda tracts like these makes you look pretty
>> stupid.
>
>Stupid is as stupid does...
>
>I ain't a smart man, but I has been lucky enough to makes it thru
>medicul skool. Good or bad, rite or wrong, smart or dum, I is trewly
>beleevin whats I is sayin. I thanks you thow for sharin your hi
>minded thawts with me. Perhaps tho, I jus am incapable of
>understandin such wonders as you do seems to know so well. Someday I
>juz hopes to be a smart as you is.
>
>> Ron Okimoto
>
>
>Sean ; )
>
I wish you weren't serious about this post. It makes you look moronic, but
that is how you actually are. Getting through medical school doesn't make you
intellectually honest. It isn't my fault that you chose to use your ability to
lie to people, and confuse people like Zoe.
It could be that you are just ignorant or stupid, but I don't believe that.
Ron Okimoto
David Jensen
muz...@aol.com (zoe_althrop) wrote in
<3dbb562f....@news-server.cfl.rr.com>:
Once I saw that he dishonestly included some frauds on his page, I saw
no reason to read the rest of it. Piltdown Man and Nebraska Man are not
part of science. If the good doctor doesn't know that, then he is
hopelessly confused. If he knows it but implies by positioning that the
rest of the evidence is equally suspect, then he is being utterly
dishonest.
Of course, no honest critic of science would refer to 50 year old books
and selected anti-science literature, but refuse to reference current
science journal articles. I doubt that he actually read the Richmond
paper.
zoe_althrop
wrote:
snip>
>>>Why is it that you think that what Sean writes is OK, but nothing anyone
>>writes
>>>correcting your misconceptions about isochrons seems to register with you?
>>
>>I don't know what you mean. I think Jon Fleming is a great teacher,
>>and so would Bjoern be if he weren't so cantankerous. Eric Rowley is
>>good, too, as is Drearash. I've learned a lot from these guys. The
>>only problem they have with me, I guess, is that I take my learning
>>and do with it as I please when it comes to final conclusions.
>
>They may be very good teachers, but you haven't let yourself learn very much
>have you?
I think what you mean is that I haven't allowed my learning to lead me
to YOUR conclusions.
>Can you see why even the guys at the ICR think that Isochron is a
>big problem for them and that they really have no good argument against it?
I don't know what the guys at the ICR think. I don't read them, not
because their arguments are necessarily wrong, but because I want to
form my own conclusions for myself.
But tell me, since you seem to know, have the ICR guys actually said
that they thought the isochron is a big problem for them? And if so,
what problems do they see? Or do you recommend that I go read their
views on the isochron?
>They can only resort to what you try and do, and claim that things are that way
>for some unknown reason or just by chance.
I certainly have not said that my premise for the isochron is due to
an unknown reason or just by chance. I've given the reason for my
premise -- that radioactive decay, which is constant, is reflected on
the isochron's graph by trajectories of decay from P to D. What fault
do you see in that statement?
And based on that premise, I have suggested that the sample whose P
has decayed to near zero will have its trajectory end up at the
Y-intercept, and since radioactive decay is constant, the trajectories
of the other samples will have their intercept correspond to the
approximate intercept of the exhausted-P sample. True, there should
be a small jump out of line, but the acceptance of small scatter in
the real world would raise no red flags to the isochronist, and the
new intercept (which lies close to the exhausted sample) will
automatically be accepted as oldD/Di, even when oldD/Di's position on
the Y-axis continues to remain at its original level.
>How reasonable is it that all of
>these rocks have just the right amounts of parent and decay products just by
>chance,
not by chance. Radioactive decay is constant the world over, and if
decay began at the formation of the Earth, it would continue to
accumulate at the same pace in all rocks. Remelting fuzzies the
picture, especially with reference to isochrons that use samples with
gases like argon.
> and that some rocks can be cross dated using different isotopes?
same reason as above.
snip>
>>that would be a problem, yes, if the perspective is one of needing
>>millions of years to evolve. But humans can vary in their sequences
>>over a short period of time if they have been programmed to vary from
>>the beginning. No need for all that time.
>
>If you had some evidence to back up this assertion you might have something,
>but since you don't it is a worthless assertion.
consider the variation that develops instantly from intermarriages.
There is no such thing as a true race, and intermarriages confirm
this. I think you know this already and are just testing me, right?
>>>Are Neandertals human?
>>
>>I would guess yes -- a different species of human, but still human. I
>>mean, just recently, I saw a taxi driver, a living, breathing human
>>taxi driver, whose cranium was shaped like some of those early
>>drawings of ancient hominids -- the brow projected far out above the
>>eyes, hung low, and sloped back, with very little forehead in
>>evidence. If he were to die and be found a few years from now, he
>>would probably be considered some kind of missing link. Yet there he
>>was, driving a car and acting like any other normal human being.
>
>You have some weird concept of sampling error.
I think there is plenty room for sampling error when just three or
four Neanderthal mtDNA sequences have been examined against a mere 70
individuals worldwide. See Science, 16 February, 2001, under the
illustration titled "The global family." This is an article by Svante
Paabo. Quote: "A network illustrating the relatedness of a series of
DNA sequences within a 10,000-base pair segment of the human X
chromosome samples from 70 --" (70!!) -- "individuals worldwide." p.
1220.
> What type of modern human is
>the most likely to fossilize today?
those swept away by some flood, maybe, including our taxi-driver
Neanderthal friend.
>Wouldn't you expect the most common type
>to be the most common type to also fossilize. This would be the same today as
>it would be thousands of years ago. Why can all Neandertals be grouped
>together whether they are found in the middle east or Europe?
ALL grouped together? In a single group of three? Or three groups of
one each? That's a rather sweeping conclusion to draw from less than
a handful, don't you think?
>These aren't
>just funny looking modern humans or we would find modern humans mixed in with
>them.
how is it possible to find modern humans mixed in with humans from a
past era? Modern humans are stuck in today's setting. It would be a
shock to find modern humans alongside human races from any other era.
This is common sense, not science.
>>>Are they some other creation?
>>
>>probably a result of inbreeding so that certain features and
>>characteristics became more pronounced.
>
>I assume that your evidence for this is with your evidence for your other
>assertions of similar value.
I guess I'm going to have to pull out my Anatomy and Physiology next
and quote from the chapter on genetics?
>>>Why aren't they mentioned in the Bible?
>>
>>the Bible is written for other purposes than science, but it does
>>mention that there were giants in those days, some called Nephilim,
>>others Rephaim, and so on.
>
>You have a pretty low opinion of the gods of the Bible if you think that
>Neandertals are the half gods.
there are many gods, false gods, and the Bible recognizes them as
such. But there is only one true God, the Creator of the Heavens and
the Earth.
But, at any rate, why do you consider the Nephilim to be gods? They
were merely a superior race descended from giants in the earlier part
of Earth's history.
>>snip>
>>
>>>>>We do have pretty good ideas as to the limits of variability in modern
>>>>>humans.
>>>>
>>>>where did these ideas come from? Which eyewitnesses? Can they be
>>>>trusted?
>>>
>>>We have sequences for thousands of humans from all the different continents.
>>
>>>It is a fact that the Neandertal sequences fall outside of the variation
>>that
>>>we have observed. No, we probably never will have the DNA sequences for the
>>>billions of people that currently exist, but if you are willing to fund such
>>a
>>>study I'm sure that you will find a group of researchers that would be
>>willing
>>>to sequence much larger sample sizes.
>>
>>how much does it take to finance such a quest? Let me check my
>>piggybank.
>
>About 40 dollars a sample would do it, but it used to cost more when most of
>the work was actually done. This assumes that collecting the samples doesn't
>cost a whole lot.
well, they seem to have drawn some pretty conclusive opinions already
from their 70 sequences (no, not thousands). But to get a more
representative sampling, you would probably need to sample a couple
million or so, I imagine? You mean, you can't get the government to
fund a project for a mere $40 million?
>>>How do you think that you cross check for contamination? My wife worked in
>>a
>>>lab where they were sequencing a lot of human D-loop sequences looking into
>>the
>>>origins of native Americans. They all knew what haplotype they were. I'm
>>sure
>>>that the people doing the Neandertal work know that they do not have
>>Neandertal
>>>type mitochondrial DNA to contaminate the samples with.
>>
>>did they know the haplotypes of the workers who helped dig up these
>>bones?
>
>Zoe you keep making this blunder and you don't even realize what you are doing.
> We have sufficiently sampled the extant human race to know that it is unlikely
>that we will find Neandertal like samples in any extant human.
and what is your source for this number? Please give it to me so I
can see how it stands up against Paabo's statement that only a few
studies of nuclear DNA sequences have been done. Quote:
"Fortunately, from the FEW studies of nuclear DNA sequences, it is
clear that what is called 'race,' although culturally important,
reflects just a few continuous traits determined by a tiny fraction of
our genes." Pp. 1219, 1220.
>I'd like to
>find some, it wouldn't bother me a bit. We share some of our MHC alleles with
>chimps.
and don't forget the mouse, with whom we "share" just as much.
>Some of the variation in our genomes is very ancient. There is no law
>that says that we can't maintain such variation by just dumb luck or by
>selection. If our ancestors had this variation we could have this variation.
>It is that thing called common descent.
this last, you must agree, is pure speculation, not science.
>If Neandertal sequences exist in the current population they would have to be
>very rare. It is very unlikely that the people that found and preped the bones
>all had someone with Neandertal DNA in the group. One group is a possibility,
>but all the research groups is not at all very likely.
ALL the research groups -- meaning your three or four? That is too
much weight given to a two-legged stool.
>Neandertal like
>sequences probably do not exist in the current human population.
speculation, pure speculation.
>If contamination were a problem why would only the Neandertal like sequences be
>recovered?
because there might be many more Neanderthal sequences in the human
population than we thought? Of course, that is pure speculation on my
part, also, for what it's worth.
>>>You could do this research yourself if you don't trust the people doing it.
>>>You don't have to have any evolutionary conceptions to just go out and find
>>out
>>>what exists out there. Do you think that the automated DNA sequencers are
>>>biased and only give the results that we want?
>>
>>no, but four or five samples are insufficient when the comparison is
>>being made to billions of humans. I mean, if a few million
>>Neanderthal sequences had been obtained, then you would have more of
>>an ability to tell if they all fell outside human sequences or if many
>>crossed over.
>
>Zoe, you don't need millions of Neandertal sequences and you know it. Just two
>from different locations and you have a pretty good idea. Three is better,
>etc. Why would only the Neandertal sequences that fall outside of the range of
>modern humans be the ones that are found? Why can't you go out and pick three
>different living humans at random and find at least one Neandertal like
>sequence?
because 70 human sequences are insufficient to come to a conclusion
yet.
> I haven't kept up with the research,
you can say that again -- and yet you jump all over Sean?
> but I'd bet the number of
>extant human sequences number in the tens of thousand
no, a mere 70.
> without finding a single
>sequence like Neandertal, and these researchers have been looking for
>diversity. What you seem to be missing is that by sampling just these few
>thousand humans they have actually sampled hundreds of millions.
Ron, you continue to build your theory on pure speculation. It is not
thousands. Back up.
>If one of
>your very distant cousins has been included in the testing and you share some
>great, great, great maternal grandmother, you have been sampled too. All of
>their extant maternal relatives have also been sampled. They haven't just been
>looking at some small inbred population, they have been covering the globe to
>get their samples. It is a possibility that we will find other mitochondrial
>types, but these types will be rare if they exist.
well, here stands one witness, Ron Okimoto, who is testifying, not
even by hearsay, but by "I think so-say." Of course, this is familiar
verbiage since a lot of evolutionary theory is couched in similar
terms -- "It is a possibility"....
>>>>> All existing Neanderthal sequences fall outside those limits.
>>>>
>>>>all four or five of them, right. I'm impressed by your
>>>>four-person-high mountains of evidence.
>>>
>>>Considering the evidence that you have, it is a mountain, isn't it?
>>
>>the evidence I have is the same evidence you have, except that you
>>have chosen to draw what I would consider to be premature conclusions,
>>and I have chosen to leave the door wide open.
>
>You can't evaluate the evidence in a coherant fashion.
I consider the Science journal to be very coherent.
>It is your bias that is
>the problem and not mine or any other scientist.
but, Ron, you are definitely biased towards the idea that thousands of
human sequences have been done. Do you think your bias is in the way
here?
>I'd like to think that at
>some level you realize this, but from your past posts this would seem unlikely.
>
>>
>>>Explain
>>>the evidence that we have. Why complain that we don't have enough if it is
>>>enough to say that you are full of baloney. Give an explanation for the
>>>Neandertal sequences that is consistent with your model. If you can't
>>explain
>>>a couple of sequences, what makes you think that you could explain 10 or a
>>>hundred?
>>
>>10 or 100 would just barely begin to allow some general pattern to
>>form.
>
>You have to take all the data into consideration and look at the pattern. If
>we just had 10 modern humans and 3 or 4 Neandertals you would have a point, but
>you know that this is not the case.
it's almost that bad. 70 modern humans and 3 or 4 Neanderthals do not
a theory make.
>>>Why do you think that you have a chance of coming up with something
>>>that would negate the results when they come from different countries and
>>from
>>>fossils from different time periods?
>>
>>I don't understand your question. Besides, I am not trying to negate
>>any results in this thread. I just mentioned that I thought the post
>>was excellent.
>
>Most people that have read your posts, realize that your endorsement isn't
>worth much.
it is worth everything to me, who is the person that matters when it
comes to my convictions. I am not trying to be worth much to anybody
else here, okay?
>What is the most excellent part of his Neandertal blather? Nothing that you've
>come up with so far seems to be any good.
The most excellent part of his most intelligent "blather" is that you
evolutionists are making some mighty premature decisions on some very
sparse data.
snip>
>This is just a fact. If that is being a curmudgeon then I'm a curmudgeon.
>Pitman knows better. He only does the things that he does to bolster his world
>view. He doesn't do it to learn more about the world,
I don't see you trying to learn more about the world, Ron. Just a few
lines above, you admit to not keeping up with research -- "I haven't
kept up with the research," you say, and yet you jump all over Sean.
> in fact his writings
>have exactly the opposite effect on anyone that reads them and thinks that they
>have some value, such as a person like yourself. This is vile. Pitman
>shouldn't have to obfuscate, he shouldn't have to be dishonest with people like
>you. You would believe anything that he writes, just as long as his
>conclusions matched yours,
not at all. I don't agree with him when he says that races clump
together according to their sequences. Paabo says in that same
article, "The network demonstrates that people from different
continents often carry identical DNA sequences. Consequently, how a
person looks gives little or no clue to what alleles he or she may
carry at any particular locus." P. 1220
or "...from the perspective of nuclear genes, it is often the case
that two persons from the same part of the world who look
superficially alike are less related to each other than they are to
persons from other parts of the world who may look very different." P.
1220.
But his main point is valid, imo, that you cannot draw the kind of
conclusions you have drawn based on the kind of data you presently
have. So far, Neanderthals do not give anywhere near conclusive
evidence of being a different species.
>so why does he write these essays? Why does he fill
>them full of crap?
are you saying that his account of the various hoaxes are lies?
>He only deceives people like yourself. He certainly
>doesn't convince anyone that understands the data that he has something of
>interest.
>
>You might be able to get dewy eyed and praise people like this, but I can't.
I didn't ask you to. But at least don't demonize them, either.
----
zoe
Jon Fleming
wrote:
>On Sun, 27 Oct 2002 01:55:37 +0000 (UTC), Sean...@juno.com (Sean
Your conclusions are not reasonable.
The data shows that a _very_ _few_ human sequences, those that are
farthest from the human average, are closer to a _very_ _few_
Neanderthal sequences, those that are farthest from the Neanderthal
average, than they are to the human average.
It _does_ _not_ show that any humans have Neanderthal DNA at all, it
just shows that a few unusual humans have DNA that is closer to _but_
_not_ _the_ _same_ as_ a few unusual Neanderthals.
It definitely shows that it is _unlikely_ that "my neighbor has
Neanderthal mtDNA -- or maybe I do". It is unlikely that your
neighbor or you have DNA that is even _similar_ to Neanderthal DNA.
>
>
>----
>zoe
Sean Pitman M.D.
> Peeked at your page. A mined quote:
>
> "Thus, the largest difference observed between any two human
> sequences was two substitutions larger than the
> smallest difference between a human and the Neandertal."
>
>
> Krings, M., Stone, A., Schmitz, R.W., Krainitzki, H., Stoneking, M. and
> Pbo,
> S., 1997. Neandertal DNA sequences and the origin of modern humans. Cell,
> 90:19.30
>
> A more recent article with input from some of the same
> authors is at
>
> http://www.eva.mpg.de/genetics/evgen/Krings_DNAseqProc1999.pdf
>
>
> Something that may have not been included in the article you
> cite, is that differences among the 9 chimp/bonobo
> samples in the study were between 1 and 81 differences.
> Differences between humans and bonobos/chimps used in
> the study ranged from 78 to 113 differences. Note that
> the lower range of human - chimp/bonobo differences fall
> within the extremes of the differences amongst the chimp/bonobos.
> Unfortunately, this is inconvenient for your argument wrt to
> Neandertal MtDNA. Now that more detail is available in a more
> recent article, shouldn't you update your page?
Actually, this finding is not "inconvenient" for my argument at all.
Take a given chimp. A chimp in the next tree might be 81
substitutions different... right? That is quite a difference for
sure. Is this vast difference due to the fact that the chimp in the
next tree belongs to a different species? Obviously not because this
same chimp might be only 78 substitutions different from a given
human... right? Based on this information alone, which is the
separate species? You see, you cannot make species judgments based on
a single phenotypic or genotypic trait. It might superficially seem
reasonable that one should be able to do so, but one might easily come
to wrong conclusions. Obviously humans are different species from
chimps/bonobos, and all chimps are from the same species despite the
fact that certain members of this species might be separtated from
each other by more substitutions than they are from members of a
different species, such as humans. So, the conclusion here is
obvious. Species cannot be determined by clusters of mutations in
hypervariable regions of DNA alone.
In any case, I will update my webpage using the numbers from this more
recent article. Thanks for the update.
Sean
gen2rev
>
> Ron Okimoto
[snip]
> > You seem to miss the point of the analysis. How you can claim that
> > certain Neandertal sequences are closer to modern humans using your
> > method is beyond good sense and reason. Find out how these analyses are
> > really done. All Neandertal mitochondrial sequences fall outside the
> > range of modern humans, but they do group with each other.
>
> Yes, I am aware of this. All Neandertals (all three of them) fall
> outside the statistical range for modern human mtDNA substitutions for
> the variable region in question. I thought I made this fact perfectly
> clear in my discussion. The three Neanderthals also group with each
> other, as humans group with each other. My point is that there exist
> living humans that are closer to the Neanderthal sequence than they
> are to other living humans. In other words, a given person might be
> only 22 substitutions different from a Neanderthal while that same
> person is 24 substitutions different from his own next-door neighbor.
> Given these three individuals alone, which one belongs to a different
> species?
I think you misunderstand what is being claimed. The level of
substitution *isn't* a linear relationship. But let me give an example.
Take three imaginary sequences:
1) ACACGT
2) TCACGA
3) ATGCGT
The difference between 1 and 2 is two substitutions. And so is the
difference between 1 and 3. But this doesn't mean that 2 and 3 are
identical. In fact, the difference between 2 and 3 is four. And becuase
of the different substitutions in different locations, it's possible to
construct a family tree based upon them. And this is precisely what the
Krings et al. paper does in Figure 7A, and if you have actually read the
paper, you will know this. A similar family tree is also shown in Figure
3 of Ovchinnikov & Goodwin referenced by Steve LaBonne elsewhere in this
thread ( http://www.promega.com/profiles/402/ProfilesinDNA_402_09.pdf ).
The fact that the range of the number of substitutions of *some* living
humans overlaps the range of the number of substitutions between living
humans and Neandertals *does* *not* mean that some living humans are
closer to the Neandertal sequence than they are to other living humans.
[snip]
Don1
> Sean...@juno.com (Sean Pitman M.D.) wrote in
> news:fd67d42a.02102...@posting.google.com:
>
> [snip]
> > The third Neanderthal who's mtDNA was successfully sequenced was found
> > in a cave at Vindija, Croatia. In 2000, scientists announced the
> > mtDNA sequencing of this third Neanderthal specimen. This new
> > sequence fell within a 3.75% cluster of the first two sequences.48
> > Modern humans cluster at around 3.5%. This is a rather narrow level
> > of diversity when one compares these clusters to chimps (15%) and
> > gorillas (19%). Various human ethnic groups also have rather narrow
> > ranges of diversity in their mtDNA sequencing. Of course, the problem
> > still remains that some humans from certain of these ethic groups are
> > more closely "related" to Neanderthals than they are to certain other
> > living humans from other groups. The question remains as to who
> > should be classed as a separate species?
>
> This is not true. The mtDNA for the Neandertals was equally distant
> from the various groups of humans.
>
> From the _Nature_ publication of the second Neandertal individual:
>
> The Feldhofer and Mezmaiskaya Neanderthals were separated
> geographically by over 2,500 km. Given that these two individuals
> contained closely related mtDNA, which is phylogenetically distinct
> from modern humans, and displays only a moderate level of sequence
> diversity compared with some primates13, these data provide further
> support for the hypothesis of a very low gene flow between the
> Neanderthals and modern humans. In particular, these data reduce
> the likelihood that Neanderthals contained enough mtDNA sequence
> diversity to encompass modern human diversity.
>
> The 'out-of-Africa' hypothesis for the origin of modern humans
> predicts equal distances between the Neanderthal sequences and
> all modern sequences. We observed this in our analysis--the
> average pairwise differences between the Neanderthals and 300
> randomly selected Africans, Mongoloids and Caucasoids were
> calculated to be 23.09+/-2.86, 23.27+/-4.06 and 25.45+/-3.27,
> respectively.
>
> http://www.nature.com/cgi-
> taf/DynaPage.taf?file=/nature/journal/v404/n6777/full/404490a0_fs.html
>
> The third Neandertal further supported this. See Chris Stringer's
> comments at
>
> http://news.bbc.co.uk/1/hi/sci/tech/967119.stm
There was a miscomminucation here due to the doctor's ambiguous
sentence "...that some humans from certain of these ethic [sic]
groups are more closely 'related' to Neanderthals than they are
to certain other living humans from other groups."
As an example, consider human group "a" who are a small subset of
ethnic group "A." Consider also, human group "b" who are a small
subset of ethnic group "B." The doctor is claiming that the
specific Neandertal mtDNA is more closely related to human group
"a"'s mtDNA than mtDNA a is to mtDNA b.
He bases his conclusion on the entire range of variation of the
substitutions in the mtDNA for human. Even though there were means
and standard deviations for the human species and for Neandertal,
which did not overlap with, for example, (mean +/- 3*stdev), the
entire range (according to the doctor) did in fact overlap. He
then claims that therefore some humans are closer to Neandertal
than those humans are to some other humans.
A criticism of overlapping ranges is a fair statistical criticism,
especially since somewhere there is an N=1. However, maybe the
doctor is confused about what the ranges mean? I know that I am.
Some details about these numbers are certainly left out. Could
someone clarify this point?
Thanks,
Don
Don1
The doctor has used overlapping ranges of human and Neandertal to
conclude that Neandertals are human. Now, I am hearing that human
and chimps ranges also overlapped. So, basically, if Neandertals
are human, then humans are chimps.
Don
Ursus: "What is more dangerous than famine, Doctor?"
Zaius: "The unknown."
("Beneath the Planet of the Apes" 1970)
Sean Pitman M.D.
> This is just another one of your crappy views of reality. I don't have
> time to tell you where you are obviously wrong, but you have wasted quite
> a bit of time for no reason.
Even from your perspective, I fail to see how I have "wasted time." I
can be used by you as a clear example of how those who don't see
things accroding to an evolutionary viewpoint are "nuts." Your
comebacks to my feeble mutterings can be used as examples of how to
answer the crazy thoughts and claims of illogical
anti-evolutionists/design theorists/creationists. So, your time is
not wasted, even if I am personally incapable of understanding your
brilliance. Because, others will certainly recognize it for what it
is.
> Just read the papers on Neandertal DNA.
I have read a few actually.
> You can't find a single one that claims to get DNA from 120,000 year old
> Neandertal fossils.
Yes, that is true. The claims are that mtDNA was obtained from
Neandertal bones ranging in ages from 30,000 to 50,000 years.
However, the reason I comment on DNA decay rates is because claims for
the isolation of DNA dating millions of years have also been made by
scientists (ie: From insects in amber etc.). The relatively rapid DNA
decay rates also significantly limit the number of Neandertal
specimens from which DNA can be successfully isolated. From what I
have read, only three Neandertals have been found to have DNA that is
preserved well enough to sequence. It seems like environmental
conditions have to be just right or the relatively fragile DNA won't
last even a few hundred years, much less tens of thousands of years.
> What you do find is that bones from warmer climates
> no matter what their age are less useful to these analysis than the bones
> from Europe. Conditions have a lot to do with preservation.
Oh, I agree...
> You seem to miss the point of the analysis. How you can claim that
> certain Neandertal sequences are closer to modern humans using your
> method is beyond good sense and reason. Find out how these analyses are
> really done. All Neandertal mitochondrial sequences fall outside the
> range of modern humans, but they do group with each other.
Yes, I am aware of this. All Neandertals (all three of them) fall
outside the statistical range for modern human mtDNA substitutions for
the variable region in question. I thought I made this fact perfectly
clear in my discussion. The three Neandertals also group with each
other, as modern humans group with each other. My point is that there
exist living humans that are closer to the Neandertal sequence than
they are to other living humans. In other words, a given person might
be only 22 substitutions different from a Neandertal while that same
person is 24 substitutions different from his own next-door neighbor.
Given these three substitutions patterns alone, which one belongs to a
different species?
> This just
> means that all Neandertals that have been sequenced are more closely
> related to each other than they are to any extant human.
Yes, they are. But, ethnic clustering also occurs and can
theoretically occur between ethnic groups that are more different in
the number of mtDNA substitutions than some of these same groups are
different from Neandertal mtDNA. Given such wide ranges of possible
substitution differences, how can one determine which ethnic group
should be classed as a separate species?
> They are
> related to us, they fall between modern humans and chimps.
Actually, Neandertals do NOT fall between modern humans and chimps.
Check your references. Neanderthals actually fall farther away from
chimps than humans do as far as substitution differences in the
particular variable region in question ("hypervariable region II").
From the "modern human" perspective, there are fewer differences, on
average, between us and Neandertals than there are between us and
chimps. Likewise, from the Neandertal's perspective, there are also
fewer differences between Neandertals and humans than between
Neandertals and chimps. It gets interesting however when you look at
it from the chimp's perspective. From the chimp's perspective, there
are fewer differences between chimps and modern humans than between
chimps and Neandertals. Using this logic, it is the modern human that
is more closely related to the chimps than Neandertals are.
> What a waste
> of a brain. You seemed to have some promise in the beginning, but you
> are becoming lamer as time goes on. You must realize at some level that
> the reason for this is because your position is so weak that trying to
> support it with propaganda tracts like these makes you look pretty
> stupid.
Stupid is as stupid does...
I ain't a smart man, but I has been lucky enough to use whats I has to
makes it thru med skool. Good or bad, rites or wrong, smart or dum, I
is trewly beleevin in whats I is sayin. I thanks you tho for sharin
your hi minded thawts with me. Perhaps tho, I jus am inkapable of
understandin such wonders as you do seems to know so good. Someday I
juz hopes to be as smart as you is.
> Ron Okimoto
Sean
Harlequin
news:3dbbec64....@news-server.cfl.rr.com:
> On Sun, 27 Oct 2002 05:02:55 +0000 (UTC), poke...@aol.com (Pokemoto)
[snip]
> And based on that premise, I have suggested that the sample whose P
> has decayed to near zero will have its trajectory end up at the
> Y-intercept, and since radioactive decay is constant, the trajectories
> of the other samples will have their intercept correspond to the
> approximate intercept of the exhausted-P sample. True, there should
> be a small jump out of line, but the acceptance of small scatter in
> the real world would raise no red flags to the isochronist, and the
> new intercept (which lies close to the exhausted sample) will
> automatically be accepted as oldD/Di, even when oldD/Di's position on
> the Y-axis continues to remain at its original level.
[snip]
Zoe, it is amazing the mental gymnastics that you will go though
to avoid the isochron. It would take trillions of years
for all the parent isotope to have all decayed if we are using
Rb-Sr (49 billion year half-life), Sm-Nd (106 billion year half-life),
Lu-Hf (36 billion year half-life), or Re-Os (43 billion year half-life).
You appear to be imagining the trajectory of a single point without
calculation where all the other points will be at the same time.
By the time that enough time has passed to drive one of those points that
was not initially by the y-intercept to being on the y-intercept (within
measurement errors) the entire isochron will have a very high slope and
thus the entire isochron will be close to the y-intercept. The result
of such a test is likely to be "infinite" age.
Here is some homework for you.
Let us imagine the following diagram.
|
|
|
|
|
|
a'
|
| a b c d e
|
|
|__________________________
a, b, c, d, and e are the points at time zero.
a' is where a will be in the far distant future (of time zero).
(It might be actually lower or higher up on the y-axis since
the exact location where a's tragectory will hit the y-axis will
have to be calculated.)
The your homework problem is to figure out where b', c', d',
and e' are. Plot those points and see what the isochron looks
like. What kind of date would the isochron method give? Remember
the the higher the slope the higher the age. And then what if there
is scatter? If the points are scattering over the y-axis then the
"age" given by the method will by infinite which is nothing more than
saying older than what are equipment and methods can measure.
You can make up your own numbers if you like. But if you want numbers,
say that we are doing Rb-Sr, that Sr-87/Sr-86 is 0.7 for a through e,
and that the Rb-87/Sr-86 values of a through e are 0.1, 0.2, 0.3, 0.4.
and 0.5 respectively.
[snip]
> I think there is plenty room for sampling error when just three or
> four Neanderthal mtDNA sequences have been examined against a mere 70
> individuals worldwide. See Science, 16 February, 2001, under the
> illustration titled "The global family." This is an article by Svante
> Paabo. Quote: "A network illustrating the relatedness of a series of
> DNA sequences within a 10,000-base pair segment of the human X
> chromosome samples from 70 --" (70!!) -- "individuals worldwide." p.
> 1220.
[snip]
I am looking at the original paper in _Cell_ that first announced the
Neandertal mtDNA. They compared the Neandertal sequence to
"994 contemporary human mitochondrial lineages, i.e. distinct
sequences occuring in one or more individuals, found in
478 Africans, 510 Europeans, 494 Asians, 167 Native Americans,
and 20 individuals from Australia and Oceania..."
In short you are completely wrong that only 70 human were compared.
The number for the 1997 paper was, adding them up from above, 1669
individual people representing 994 distinct sequences.
And even if it was just 70, your case would still be weak. Do you
think that by chance they picked just freek individuals to sequence?
The odds of that happing are almost impossibly low.
In any even lets go back to the data from the original _Cell_ paper.
When comparing the differences between the 994 human lineages,
they found they an average of 8.0+/-3.1 differences with the
range being from 1 to 24. (And if they compared people the
range would obviously been from 0 to 24. Doing the same
between the human lineages and the Neandertal gave
27.2+/-2.2 with a range of 22 to 36.
Now you will say that they overlap. True, but that does not make
Neandertals in modern humans. First of all let notice just how
rare it was for the human-human comparison were larger than human-
Neandertal comparisons.
"In total, 0.002% of the pairwise comparisons between human mtDNA
sequences were larger than the smallest difference between the
Neandertal and a human."
Second, the difference between the Neandertal and the African,
Asian, American, and Australian/Oceanic lineages were approximately
the same, just as what you would expect if Neandertals and modern
humans made up distinct populations of individuals.
And as has been pointed out by others, it is not just the
absolute number of differences that counts. What the actual
differences are is very important too. This brings up the need
for a phylogenetic analysis.
To be able to use data from 16 chimpanzee lineages the number of human
lineages was reduced to 986. Then the 16 chimp lineages, the Neandertal,
and the 986 human sequences were used for a phylogenetic analysis. The
chimp lineages were used to root the tree -- in other words it was
assumed that chimps are distinct from the human/Neanderal group.
The result was was that Neandertals are distinct from humans.
And I don't think I have to mention that since the 1997 paper _Cell_
paper the data set that one can use has grown: the original authors
sequences another mtDNA sequence from the same individual and other
groups have sequenced other Neandertals. And more sequencing of
humans, chimps, and other primates has occured as well. And yet
the conclusion has only become stronger.
The publication of the second Neandertal individual is at
http://www.nature.com/cgi-
taf/DynaPage.taf?file=/nature/journal/v404/n6777/full/404490a0_fs.html
In particular the results of their phylogenetic analysis can be seen
in the diagram at
http://www.nature.com/nature/journal/v404/n6777/fig_tab/404490a0_F3.html
Notice that 5846 modern humans were used in this study representing
1,897 distinct sequences. The Neandertal mtDNA is still quite
distinct from humans mtDNA.
Also of interest is http://www.pnas.org/cgi/content/full/96/9/5077
which shows just how undiverse humans are compared to other
hominoids (i.e. apes). "Several chimpanzee and bonobo clades
(and even single social groups) have retained substantially
more mitochondrial variation than is seen in the entire human
species." This is very inconsistent with YEC dogma that
Pitman, AiG, ICR, and others would have us believe.
Sean Pitman M.D.
> >> This is just another one of your crappy views of reality. I don't have
> >> time to tell you where you are obviously wrong, but you have wasted quite
> >> a bit of time for no reason.
> >
> >Even from your perspective, I fail to see how I have "wasted time." I
> >can be used by you as a clear example of how those who don't see
> >things according to an evolutionary viewpoint are "nuts." Your
> >comebacks to my feeble mutterings can be used as examples of how to
> >answer the crazy thoughts and claims of illogical
> >anti-evolutionists/design theorists/creationists. So, your time is
> >not wasted even if I am personally incapable of understanding your
> >brilliance, because others will certainly recognize it for what it is.
>
> I have to disagree, your writing are dishonest and misleading. You only have
> to look at responses like Zoe's to figure that out. I've said to Zoe that I
> think that what you are doing is vile and I meant it.
Wow! "Vile"? Hmmm... It almost sounds as if you are defending
evolution as some sort of moral position... a religion perhaps? You
know Ron, I disagree with you strongly on many things that you say,
but I do think that you honestly believe that what you say is true.
Perhaps you should give me that same benefit of the doubt? I think
that your statements are also misleading, but that you are not aware
of this, because you honestly think that what you say is true. You
may also think my statements are misleading according to your
perspective, but at least you should consider that I might actually
honestly believe what I am saying.
> >> Just read the papers on Neandertal DNA.
> >
> >I have read quite a few actually.
>
> You may have read them, but you obviously do not understand them.
Obviously not. Of course, you must give me some credit for presenting
my misguided thoughts to this forum for clarification since most of
those that contribute to this forum strongly disagree with me. At
least I don't hide under a rock somewhere and shelter myself by only
talking with those who hold my same viewpoint.
> >> You can't find a single one that claims to get DNA from 120,000 year old
> >> Neandertal fossils.
> >
> >Yes, that is true. The claims are that mtDNA was obtained from
> >Neanderthal bones ranging in ages from 30,000 to 50,000 years.
> >However, the reason I comment on DNA decay rates is because claims for
> >the isolation of DNA dating millions of years has also been made (ie.
> >from insects in amber). The relatively rapid DNA decay rates also
> >limit the number of Neanderthal specimens that DNA can be successfully
> >isolated from... significantly. From what I have read, only three
> >Neanderthals have been found to have DNA that is preserved well enough
> >to sequence. It seems like environmental conditions have to be just
> >right or the relatively fragile DNA won't last even a few thousand
> >years, much less tens of thousands of years.
>
> So what, you are just admitting to obfuscating the issues.
>
> The decay rates don't matter if we actually find some DNA
> to sequence does it?
Actually, I think that understanding the relative fragility of DNA as
well as its fairly rapid relative decay rate, is an important part of
understanding why it is so hard to find Neandertal specimens with
adequately preserved DNA. This issue also speaks to the fact that DNA
finds, that claim to have found DNA in specimens supposed to be
millions of years old, are highly questionable. This problem is not
generally told to the public. That is why movies like Jurassic Park
have contributed to the false impression that the public has as to the
survivability of intact DNA.
> >> What you do find is that bones from warmer climates
> >> no matter what their age are less useful to these analysis than the bones
> >> from Europe. Conditions have a lot to do with preservation.
> >
> >Oh, I agree...
> >
> >> You seem to miss the point of the analysis. How you can claim that
> >> certain Neandertal sequences are closer to modern humans using your
> >> method is beyond good sense and reason. Find out how these analyses are
> >> really done. All Neandertal mitochondrial sequences fall outside the
> >> range of modern humans, but they do group with each other.
> >
> >Yes, I am aware of this. All Neandertals (all three of them) fall
> >outside the statistical range for modern human mtDNA substitutions for
> >the variable region in question. I thought I made this fact perfectly
> >clear in my discussion. The three Neanderthals also group with each
> >other, as humans group with each other. My point is that there exist
> >living humans that are closer to the Neanderthal sequence than they
> >are to other living humans. In other words, a given person might be
> >only 22 substitutions different from a Neanderthal while that same
> >person is 24 substitutions different from his own next-door neighbor.
> >Given these three individuals alone, which one belongs to a different
> >species?
>
> You keep repeating this, but it is just wrong. There isn't a single human
> sequence that is closer to Neandertal than it is to another human. You are
> just looking a gross similarity. This is bogus and if you knew
> anything about DNA sequence you would know that it is bogus.
It seems to me Ron, that you have not carefully read the literature
available. Consider some other replies to this particular discussion
and you will note that the range for human variation is greater than
the smallest difference between a modern human and the Neandertal
sequence. That means that some humans match the Neandertal sequence
more closely than they match certain other humans living today.
(Krings, M., Geisert, H., Schmitz, R., Krainitzki, H., and Pääbo, S.
DNA sequence of mitochondrial hypervariable region II from the
Neandertal type specimen. Evolution, Proc. Natl. Acad. Sci. USA, Vol.
96, pp. 5581-5585, May, 1999.)
> Demonstrate that
> what you claim is true. Find a modern human sequence that is closer to
> Neandertal than it is to another extant human. You claim that they
> exist, but only by using the wrong measure. Just because sequences differ by
> the same number of substitutions doesn't mean that the substitutions are the
> same. Even though two modern human sequences can differ by 24 substitutions
> they are different substitutions than the 22 that the closest human and
> Neandertals differ by. These are three different individual modern humans.
Are you saying that, depending on the type of substitution difference,
individuals with wider separations can be more related than those with
fewer total differences? If so, this is a far different theory than
that proposed by every journal that has reported on this topic (At
least the ones that I have come across). Perhaps you should write
your own paper based on this hypothesis of yours. Personally, I think
that it is weak. If you are correct, no one should be talking about
absolute numbers at all, but strictly about the types or qualities of
substitutions involved. For you, absolute numbers mean nothing? Very
interesting take on the issue. At least it admits the problem with
the use of absolute numbers. And that, in my book, is a step in the
right direction.
> Your interpretation of the data is bogus. Get the sequences and look at them
> yourself. None of them will be closer to Neandertal than they are to another
> extant human being. If they are 24 substitutions from eachother they will
> likely be more than 24 substitutions from Neandertal.
You are wrong in this statement Ron. In fact, a more recent analysis
shows that the variation range for humans is between 1 and 35. There
are in fact humans living today, although rare, that are farther from
some other humans living today than they are from Neandertal mtDNA
sequences by a margin of 5 or 6 (Krings et al., 1999. above
reference).
> Not only that, but the
> sequences will nest within modern humans and will not be found to be from the
> Neandertal lineage.
Nesting is a different issue entirely. Ethnic groups and even family
groups also have nested DNA sequences, and yet they belong to the same
species. Nesting, by itself, does not establish the existence of a
new species.
> You do know about common descent and nested similarity,
> don't you? You are using a stupidly simple measure of difference and drawing
> the incorrect conclusion from it.
"Stupidly simple"? I am using the same measure of differences used by
those who are publishing the data. If my measure is stupid, then,
according to your statement, their measures are stupid as well... and
that is my whole point.
Nesting is the minimum requirement to assume common decent. However,
nesting does not PROVE common decent. Similar DNA nesting can be
found in very different phenotypic creatures and very different
nesting patterns can be found within different groups contained within
the same species. Phylogenies based on genetic analysis and nesting
patterns are not always intuitively clear.
> >> This just
> >> means that all Neandertals that have been sequenced are more closely
> >> related to each other than they are to any extant human.
> >
> >Yes, they are. But ethnic clustering also occurs and can
> >theoretically occur between ethnic groups that are more different in
> >the number of mtDNA substitutions than some groups are different from
> >Neanderthal mtDNA. Given such wide ranges of possible substitution
> >differences, how can one determine which ethnic group should be
> >classed as a separate species?
>
> So what? You are misinterpreting this data. It does not mean what you think
> that it does. You are wrong and your analysis is bogus. You obviously
> do not understand what you are talking about. We would not
> class different ethnic groups as different species. Why would we?
Exactly. Why would we? However, based in absolute differences, they
are sometimes more different than the differences that exist between
some of these groups and truly different species.
> The sequences would still nest within humans and not outside
> of humans no matter the gross differences between them.
Again, this is not the assumption made by the authors writing up their
conclusions on their own work. They make their conclusions based on
the "gross differences", and not, as you suggest, on the exact type of
differences found.
> We
> don't expect equal and constant evolution in all lineages. You really
> don't understand how the analysis is done. A sequence derived from one
> ancestral sequence will look different from one derived from a different
> ancestral sequence. Long branch lengths tend to collapse the branch lengths
> and make distantly related sequences more similar than they really are, and
> this occurs in the D-loop sequence, but we can still tell that the Neandertal
> sequences are derived from a different starting point. How else do you think
> that we can tell that the humans sequences derive from one that
> existed 75,000 to 150,000 years ago and the Neandertal sequences derive from
> one that existed half a million years ago?
The actual numbers given by Pääbo et al. are 111,000 and 260,000 years
for the date of modern human divergence, and 317,000 and 741,000 years
for human-Neandertal divergence. The date of Neandertal-human-chimp
common ancestor was taken as a given to be around 4-5 million years
ago. The rate of mutation for the region in question was calculated
at 0.94 x 10^-7. The Tamura-Nei algorithm was used to "correct" for
multiple substitution differences. After this correction, the
resulting genetic differences were used to calculate the date of
divergence for both Neandertals from the common ancestor of humans and
for modern humans from the common ancestor of modern humans.
As it turns out, there are problems with the rate of mutation used in
this calculation. The error may be as great as 20 fold in the favor
of a higher mutation rate than previously thought. If correct, the
calculations based on this new mutation rate for mtDNA would bring the
age of the famous "Mitochondrial Eve" down from 100,000 to 200,000
years to less than 10,000 years (Gibbons, A. Calibrating the
Mitochondrial Clock, Science 279, Volume 279, Number 5347 Issue of 2
Jan 1998, pp. 28 – 29)
Besides this problem, it seems to me that the "corrections" made in
the calculations of divergent dates are not primarily used to support
the hypothesis that Neandertals belong to a different species. The
reason given for this is that the "corrections" do not change the
"general situation." In other words, the absolute range of
substitutions differences remains approximately the same. The paper
strongly urges that the absolute average differences between
Neandertals and modern humans speaks in favor of the hypothesis that
Neandertals are in fact separate species.
Now, I will agree that the evidence speaks to the common decent of
Neandertals from a different starting point than seems to be the case
for most humans living today. However, the same conclusions can be
drawn for the common decent of various families and ethnic groups
living today. These differences however, cannot be used to prove or
give evidence for species separation. I do not think that these
clustered variations and similarities that occur within a single
segment of DNA can be used as evidence of unique or separate species
boundaries since many of these same differences, to the same degree,
can be seen within single species groups living today.
> >> They are
> >> related to us, they fall between modern humans and chimps.
Obviously I agree that Neandertals are related to us. It is my
position that they are only an ethnic variation of Homo sapiens. Now,
even among evolutionists, I would say that you are on your own when
you say that Neandertals "fall between modern humans and chimps."
Neandertals are no closer related to chimps than humans are as far as
their mtDNA sequences are concerned, even given the "corrective"
changes described above. They are in fact, "approximately equidistant"
as far as their mtDNA substitution differences are concerned... if not
a bit farther since certain humans are more similar to chimp mtDNA
than the Neandertal mtDNA is.
> >Actually, Neanderthals do not fall between modern humans and chimps.
> >Check your references. Neanderthals actually fall farther away from
> >chimps than humans do as far as substitution differences. From the
> >"modern human" perspective, there are fewer differences, on average,
> >between us and Neanderthals than there are between us and chimps.
>
> Idiot. This is beneath even you. If the sequences fell where you say, why
> would modern humans be 500,000 years distant from the Neandertal type common
> ancestor and 5-8 million from the chimp human ancestor.
>
> By anyones measure this is between modern humans (75,000 to 150,000) and
> chimps.
You aren't just calling me an idiot; you are calling Pääbo and his
team idiots. Check out page 3 of the reference cited above. You will
find there a comparison table that cross-matches humans, Neandertals
and chimps/bonobos. You will note from this table that Neandertals
are no closer to chimps/bonobos than modern humans are, despite the
"corrections" used to obtain this data. In fact, you will find that
there are some humans that are closer matches to chimps/bonobos than
is the most closely matched Neandertal sequence. The closest human
match shows "78" differences while the most closely matched Neandertal
sequence shows "84" differences.
By the way, as an educated professional, as I assume that you are a
professional, even if I were an idiot as you say, it is not
professional to call an idiot, an idiot... at least not in public. It
reflects more on you than it does on the idiot.
> >Likewise, from the Neanderthal's perspective, there are also fewer
> >differences between Neanderthal's and humans than between Neanderthals
> >and chimps. It gets interesting however when you look at it from the
> >chimp's perspective. From the chimp's perspective, there are fewer
> >differences between chimps and modern humans than there are between
> >chimps and Neanderthals. Using this logic, it is the modern human
> >that is more closely related to the chimps than Neanderthals are.
>
> What a waste of a brain. You must realize your error by now. Just
> think about it for 5 minutes. You are wrong about this, and I
> can't understand how you could be this wrong.
Actually, despite my thinking about it for hours on end, I have not
realized my error as of yet. In fact, I truly do not understand how
you can maintain your position. Your arguments even seem to contradict
the standard attempts to explain this data in support of the separate
species status of Neandertals. The standard arguments attempt to show
that the absolute number of substitution differences along with the
average clustering of these differences indicate that Neandertals not
only came from a different common ancestor than most humans but that
Neandertals should also be classed as a different species altogether.
This argument fails because individual ethnic groups living today have
unique genetic differences that are different from every other ethnic
group of humans living today. Each ethnic group has descended from a
different common ancestor, but this does not mean that each ethnic
group represents a different species. Also, the absolute number of
differences does not, by default, make a particular creature part of a
separate species seeing as how these absolute numbers have overlaps
between clearly separated species. The type of mutations involved
also does not necessarily make a given creature part of a different
species as you indicate. If it does, I have yet to see it supported
in convincing manner for the case of Neandertals being a separate
species from humans. You are the first that I have heard use this
argument.
So, it is my position that a single characteristic cannot be
adequately relied upon to determine species boundaries. That is all.
I think it is an error to propose such a thing as has been done with
Neandertal mtDNA. Its superficial reasonableness makes it very
appealing and therefore one can easily be misled by it, but a more
careful investigation will show the limits of such hypotheses.
> >> What a waste
> >> of a brain. You seemed to have some promise in the beginning, but you
> >> are becoming lamer as time goes on. You must realize at some level that
> >> the reason for this is because your position is so weak that trying to
> >> support it with propaganda tracts like these makes you look pretty
> >> stupid.
> >
> >Stupid is as stupid does...
> >
> >I ain't a smart man, but I has been lucky enough to makes it thru
> >medicul skool. Good or bad, rite or wrong, smart or dum, I is trewly
> >beleevin whats I is sayin. I thanks you thow for sharin your hi
> >minded thawts with me. Perhaps tho, I jus am incapable of
> >understandin such wonders as you do seems to know so well. Someday I
> >juz hopes to be a smart as you is.
> >
> >> Ron Okimoto
> >
> >
> >Sean ; )
> >
>
> I wish you weren't serious about this post. It makes you look moronic, but
> that is how you actually are. Getting through medical school doesn't
> make you intellectually honest. It isn't my fault that you chose to
> use your ability to lie to people, and confuse people like Zoe.
>
> It could be that you are just ignorant or stupid, but I don't believe that.
I am fully aware that I look moronic to those such as yourself. You
must give me credit though for asking such idiotic questions even
though I will be called "idiot", "crazy", "liar", and much worse
actually, when in fact I am honest in my questions. If I am confused,
I am honestly confused.
> Ron Okimoto
Sean
Pokemoto
>Path:
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>From: muz...@aol.com (zoe_althrop)
>Date: Sun, 27 Oct 2002 13:59:42 +0000 (UTC)
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>
>
>>They may be very good teachers, but you haven't let yourself learn very much
>>have you?
>
>I think what you mean is that I haven't allowed my learning to lead me
>to YOUR conclusions.
Not my conclusions, but rational conclusions made by the vast majority of
existing scientists in the field. Your explanations are often so dippy that
people keep nominating you for that Chez thingy.
>
>>Can you see why even the guys at the ICR think that Isochron is a
>>big problem for them and that they really have no good argument against it?
>
>I don't know what the guys at the ICR think. I don't read them, not
>because their arguments are necessarily wrong, but because I want to
>form my own conclusions for myself.
>
>But tell me, since you seem to know, have the ICR guys actually said
>that they thought the isochron is a big problem for them? And if so,
>what problems do they see? Or do you recommend that I go read their
>views on the isochron?
Go to the institute of creation research web page and search for Isochron.
They also have some project on radiometric dating in general. Even the ICR
doesn't argue what you do. That should tell you something, but it probably
won't penetrate.
Snip:
>
>>>that would be a problem, yes, if the perspective is one of needing
>>>millions of years to evolve. But humans can vary in their sequences
>>>over a short period of time if they have been programmed to vary from
>>>the beginning. No need for all that time.
>>
>>If you had some evidence to back up this assertion you might have something,
>>but since you don't it is a worthless assertion.
>
>consider the variation that develops instantly from intermarriages.
>There is no such thing as a true race, and intermarriages confirm
>this. I think you know this already and are just testing me, right?
This has virtually nothing to do with the argument at hand. Why did you even
bring it up?
Eve had a single mitochondrial type. Demonstrate that she did not. All extant
humans are descended from Eve using your model. Where was all this variation
pre programed in?
All Eve's daughters and sons inherited her mitochondrial mitochondrial type.
This would have been the same one as Adam's because she was essentially a clone
made from Adams rib.
>
>>>>Are Neandertals human?
>>>
>>>I would guess yes -- a different species of human, but still human. I
>>>mean, just recently, I saw a taxi driver, a living, breathing human
>>>taxi driver, whose cranium was shaped like some of those early
>>>drawings of ancient hominids -- the brow projected far out above the
>>>eyes, hung low, and sloped back, with very little forehead in
>>>evidence. If he were to die and be found a few years from now, he
>>>would probably be considered some kind of missing link. Yet there he
>>>was, driving a car and acting like any other normal human being.
>>
>>You have some weird concept of sampling error.
>
>I think there is plenty room for sampling error when just three or
>four Neanderthal mtDNA sequences have been examined against a mere 70
>individuals worldwide. See Science, 16 February, 2001, under the
>illustration titled "The global family." This is an article by Svante
>Paabo. Quote: "A network illustrating the relatedness of a series of
>DNA sequences within a 10,000-base pair segment of the human X
>chromosome samples from 70 --" (70!!) -- "individuals worldwide." p.
>1220.
This is a totally different study on sex-linked DNA sequence of the X
chromosome. Do you realize that mitochondrial DNA is cytoplasmic and
maternally inherited. Do you realize that thousands and thousands of
mitochondrial sequences have been and are being sequenced. It is a lot of work
sequencing 10,000 bp from 70 individuals, but the study is testing something
else, not what you think.
What you have to ask yourself is why these different studies on different DNA
sequence tell us a consistent story about human evolution?
The X chromosome is not maternally inherited. Females get one copy from their
fathers and one copy from their mothers.
>
>> What type of modern human is
>>the most likely to fossilize today?
>
>those swept away by some flood, maybe, including our taxi-driver
>Neanderthal friend.
I said most likely. What was the most likely type to be preserved in the flood
victims?
>
>>Wouldn't you expect the most common type
>>to be the most common type to also fossilize. This would be the same today
>as
>>it would be thousands of years ago. Why can all Neandertals be grouped
>>together whether they are found in the middle east or Europe?
>
>ALL grouped together? In a single group of three? Or three groups of
>one each? That's a rather sweeping conclusion to draw from less than
>a handful, don't you think?
Probably purposely obtuse, but I can't tell.
>
>>These aren't
>>just funny looking modern humans or we would find modern humans mixed in
>with
>>them.
>
>how is it possible to find modern humans mixed in with humans from a
>past era? Modern humans are stuck in today's setting. It would be a
>shock to find modern humans alongside human races from any other era.
>This is common sense, not science.
That is all modern science claims, but YEC claims something different doesn't
it?
So you admit that the current scientific explanation is reasonable and backed
up by the current findings, but YEC claims seem to be left out in the cold?
>
>>>>Are they some other creation?
>>>
>>>probably a result of inbreeding so that certain features and
>>>characteristics became more pronounced.
>>
>>I assume that your evidence for this is with your evidence for your other
>>assertions of similar value.
>
>I guess I'm going to have to pull out my Anatomy and Physiology next
>and quote from the chapter on genetics?
No just pointing out that you have as much evidence for this assertion and any
others. It doesn't matter what you can dig up in some genetics text, but how
you are applying it. Inbreeding will not cause the genetic variation that is
observed in the Neandertals compared to modern humans. In fact it would seem
not to be inbreeding because the Neandertal sequence that we have analyzed are
about as far from each other as the most divergent modern human sequences are
from each other. These guys don't seem to be very closely related by
inbreeding. You might be better off suggesting that they were all selected
under similar environmental conditions for their genetic morphology.
>
>>>>Why aren't they mentioned in the Bible?
>>>
>>>the Bible is written for other purposes than science, but it does
>>>mention that there were giants in those days, some called Nephilim,
>>>others Rephaim, and so on.
>>
>>You have a pretty low opinion of the gods of the Bible if you think that
>>Neandertals are the half gods.
>
>there are many gods, false gods, and the Bible recognizes them as
>such. But there is only one true God, the Creator of the Heavens and
>the Earth.
>
>But, at any rate, why do you consider the Nephilim to be gods? They
>were merely a superior race descended from giants in the earlier part
>of Earth's history.
I said that they were the half gods. Reread what I wrote. They were supposed
to be the heros of old that were descended from the gods that mated with human
females.
It doesn't matter if they don't quailfy as "true" gods by your definition they
were called gods in the Bible.
Snip:
>>About 40 dollars a sample would do it, but it used to cost more when most of
>>the work was actually done. This assumes that collecting the samples
>doesn't
>>cost a whole lot.
>
>well, they seem to have drawn some pretty conclusive opinions already
>from their 70 sequences (no, not thousands). But to get a more
>representative sampling, you would probably need to sample a couple
>million or so, I imagine? You mean, you can't get the government to
>fund a project for a mere $40 million?
You know by now that you are talking about a totally different data set.
Enough said. You are very far off on this one because you do not know what you
are talking about.
Snip:
>and what is your source for this number? Please give it to me so I
>can see how it stands up against Paabo's statement that only a few
>studies of nuclear DNA sequences have been done. Quote:
>"Fortunately, from the FEW studies of nuclear DNA sequences, it is
>clear that what is called 'race,' although culturally important,
>reflects just a few continuous traits determined by a tiny fraction of
>our genes." Pp. 1219, 1220.
So what? We knew this 30 years ago using blood typing. Racial differences do
not have much of a genetic basis. This just means that we are all more closely
related to each other than some people want to believe. It says nothing about
why Neandertals fall so far outside this variation that we can't group them
within any of the known races.
Again, this is not a mitochondrial study. You are looking at the wrong
experiment.
>
>>I'd like to
>>find some, it wouldn't bother me a bit. We share some of our MHC alleles
>with
>>chimps.
>
>and don't forget the mouse, with whom we "share" just as much.
As far as I know we share no MHC alleles with mice except the ones that have
been genetically engineered to have human MHC for tissue transplantation
experiments. Our common ancestor with mice is so distant that we have no
alleles in common, but we still share alleles with chimps.
>
>>Some of the variation in our genomes is very ancient. There is no law
>>that says that we can't maintain such variation by just dumb luck or by
>>selection. If our ancestors had this variation we could have this
>variation.
>>It is that thing called common descent.
>
>this last, you must agree, is pure speculation, not science.
It is inference from the data. Just as we can pick your parents out of a room
full of people by testing their DNA, we can determine the most closely related
species to humans. We use the same inferences and data. It is science. Just
because you don't want it to be doesn't mean much to the world. If you think
that this is pure speculation what do you think of your stuff?
>
>>If Neandertal sequences exist in the current population they would have to
>be
>>very rare. It is very unlikely that the people that found and preped the
>bones
>>all had someone with Neandertal DNA in the group. One group is a
>possibility,
>>but all the research groups is not at all very likely.
>
>ALL the research groups -- meaning your three or four? That is too
>much weight given to a two-legged stool.
What do you need? It is you that are being unreasonable and you know it.
Where are these extant Neandertal sequences? Why haven't we found them? None
of the researchers involved had Neandertal sequence or they would have stated
this. Why would Neandertal sequence be the contaminant? Why wouldn't the
researchers own DNA be the contaminant? In at least two of the studies they
sent samples to an independent laboratory and the two labs got the same
sequence from the same sample. You don't have a leg to stand on in this case,
but you can't admit it. There is nothing that will satisfy you. Explain their
results. Where did the contamination come from and why is the contamination
always Neandertal sequence when they are working with Neandertal bones, but
when they work with other human remains the sequences are not Neandertal? Even
you should be able to reason through this one.
>
>>Neandertal like
>>sequences probably do not exist in the current human population.
>
>speculation, pure speculation.
I have more evidence for this than you have that they still exist. Like I said
I would like to see this variation in the extant population. The fact is that
from the samples that we have taken from all the diverse populations it is
unlikely that we will find a sequence as divergent as the Neandertal in the
extant population of humans.
>
>>If contamination were a problem why would only the Neandertal like sequences
>be
>>recovered?
>
>because there might be many more Neanderthal sequences in the human
>population than we thought? Of course, that is pure speculation on my
>part, also, for what it's worth.
Where are they?
How can they hide so well?
>
>>>>You could do this research yourself if you don't trust the people doing
>it.
>>>>You don't have to have any evolutionary conceptions to just go out and
>find
>>>out
>>>>what exists out there. Do you think that the automated DNA sequencers are
>>>>biased and only give the results that we want?
>>>
>>>no, but four or five samples are insufficient when the comparison is
>>>being made to billions of humans. I mean, if a few million
>>>Neanderthal sequences had been obtained, then you would have more of
>>>an ability to tell if they all fell outside human sequences or if many
>>>crossed over.
>>
>>Zoe, you don't need millions of Neandertal sequences and you know it. Just
>two
>>from different locations and you have a pretty good idea. Three is better,
>>etc. Why would only the Neandertal sequences that fall outside of the range
>of
>>modern humans be the ones that are found? Why can't you go out and pick
>three
>>different living humans at random and find at least one Neandertal like
>>sequence?
>
>because 70 human sequences are insufficient to come to a conclusion
>yet.
You aren't talking about the same study. Even the first Mitochondrial Eve
paper had sampled around 150 sequences and that was back in what, 1987? We
have thousands and thousands of mitochondrial D-loop sequences.
>
>> I haven't kept up with the research,
>
>you can say that again -- and yet you jump all over Sean?
I've obviously kept up with it better than Sean.
>
>> but I'd bet the number of
>>extant human sequences number in the tens of thousand
>
>no, a mere 70.
The X chromosome is not mitochondrial DNA.
>
>> without finding a single
>>sequence like Neandertal, and these researchers have been looking for
>>diversity. What you seem to be missing is that by sampling just these few
>>thousand humans they have actually sampled hundreds of millions.
>
>Ron, you continue to build your theory on pure speculation. It is not
>thousands. Back up.
You are just ignorant. This isn't bad, but you are making some big mistakes
because of it. We aren't just talking about 70 sequences. You would know this
if you had some idea of what you were talking about. Do a pubmed search using
mitochondrial DNA and humans. You can add D-loop in there to reduce the number
of hits.
>
>>If one of
>>your very distant cousins has been included in the testing and you share
>some
>>great, great, great maternal grandmother, you have been sampled too. All of
>>their extant maternal relatives have also been sampled. They haven't just
>been
>>looking at some small inbred population, they have been covering the globe
>to
>>get their samples. It is a possibility that we will find other
>mitochondrial
>>types, but these types will be rare if they exist.
>
>well, here stands one witness, Ron Okimoto, who is testifying, not
>even by hearsay, but by "I think so-say." Of course, this is familiar
>verbiage since a lot of evolutionary theory is couched in similar
>terms -- "It is a possibility"....
Demonstrate that I am wrong. It is a possibility, no one would deny that, but
it isn't a very good possiblity or we would have found these sequences already.
In more than 16 years of searching why haven't we found at least one, when the
purpose of most of the studies was to sample population variation? The studies
have sampled isolated populations from Tibet to amazon villages to Kung bushmen
in Africa. Where are the Neandertal sequences? Why are they so hard to find
if they are such a rich source of contamination?
>
>>>>>> All existing Neanderthal sequences fall outside those limits.
>>>>>
>>>>>all four or five of them, right. I'm impressed by your
>>>>>four-person-high mountains of evidence.
>>>>
>>>>Considering the evidence that you have, it is a mountain, isn't it?
>>>
>>>the evidence I have is the same evidence you have, except that you
>>>have chosen to draw what I would consider to be premature conclusions,
>>>and I have chosen to leave the door wide open.
>>
>>You can't evaluate the evidence in a coherant fashion.
>
>I consider the Science journal to be very coherent.
Wrong study, again. You can't evaluate evidence in a coherant fashion if it
doesn't even apply to the problem at hand.
>
>>It is your bias that is
>>the problem and not mine or any other scientist.
>
>but, Ron, you are definitely biased towards the idea that thousands of
>human sequences have been done. Do you think your bias is in the way
>here?
Because I know that they have been done. You cite a single paper on a
different topic. Look up Cann and Wilson (Nature 1987 Jan 1-7;325(6099):31-6)
and you will pull up the first mitochondrial Eve paper they had around 150
sequences in just this one. How many do you think have been done since then?
Do a PubMed search and find out if you don't believe me.
>
>>I'd like to think that at
>>some level you realize this, but from your past posts this would seem
>unlikely.
>>
>>>
>>>>Explain
>>>>the evidence that we have. Why complain that we don't have enough if it
>is
>>>>enough to say that you are full of baloney. Give an explanation for the
>>>>Neandertal sequences that is consistent with your model. If you can't
>>>explain
>>>>a couple of sequences, what makes you think that you could explain 10 or a
>>>>hundred?
>>>
>>>10 or 100 would just barely begin to allow some general pattern to
>>>form.
>>
>>You have to take all the data into consideration and look at the pattern.
>If
>>we just had 10 modern humans and 3 or 4 Neandertals you would have a point,
>but
>>you know that this is not the case.
>
>it's almost that bad. 70 modern humans and 3 or 4 Neanderthals do not
>a theory make.
Doesn't apply, you have the wrong study.
>
>>>>Why do you think that you have a chance of coming up with something
>>>>that would negate the results when they come from different countries and
>>>from
>>>>fossils from different time periods?
>>>
>>>I don't understand your question. Besides, I am not trying to negate
>>>any results in this thread. I just mentioned that I thought the post
>>>was excellent.
>>
>>Most people that have read your posts, realize that your endorsement isn't
>>worth much.
>
>it is worth everything to me, who is the person that matters when it
>comes to my convictions. I am not trying to be worth much to anybody
>else here, okay?
You can't be worth too much to yourself if you accept bogus junk like Sean is
handing out.
>
>>What is the most excellent part of his Neandertal blather? Nothing that
>you've
>>come up with so far seems to be any good.
>
>The most excellent part of his most intelligent "blather" is that you
>evolutionists are making some mighty premature decisions on some very
>sparse data.
This has been thoroughly discounted. It is not premature. The data stands,
and his argument is the weak one. Most of it doesn't even exist except in his
mind.
>
>snip>
>
>>This is just a fact. If that is being a curmudgeon then I'm a curmudgeon.
>>Pitman knows better. He only does the things that he does to bolster his
>world
>>view. He doesn't do it to learn more about the world,
>
>I don't see you trying to learn more about the world, Ron. Just a few
>lines above, you admit to not keeping up with research -- "I haven't
>kept up with the research," you say, and yet you jump all over Sean.
Because I have other things to do. My graduate thesis was on mitochondrial DNA
evolution. Keeping up with human evolution would be just a hobby. Sean can't
jump all over anyone because he doesn't understand the material enough to
defend it. I think that it is vile that people like Sean exist to fool people
like you. That is the only reason that I am responding to this thread.
>
>> in fact his writings
>>have exactly the opposite effect on anyone that reads them and thinks that
>they
>>have some value, such as a person like yourself. This is vile. Pitman
>>shouldn't have to obfuscate, he shouldn't have to be dishonest with people
>like
>>you. You would believe anything that he writes, just as long as his
>>conclusions matched yours,
>
>not at all. I don't agree with him when he says that races clump
>together according to their sequences. Paabo says in that same
>article, "The network demonstrates that people from different
>continents often carry identical DNA sequences. Consequently, how a
>person looks gives little or no clue to what alleles he or she may
>carry at any particular locus." P. 1220
>
>or "...from the perspective of nuclear genes, it is often the case
>that two persons from the same part of the world who look
>superficially alike are less related to each other than they are to
>persons from other parts of the world who may look very different." P.
>1220.
>
>But his main point is valid, imo, that you cannot draw the kind of
>conclusions you have drawn based on the kind of data you presently
>have. So far, Neanderthals do not give anywhere near conclusive
>evidence of being a different species.
Only in your mind and as you have demonstrated you don't have enough on the
ball to worry anyone about their conclusions of this data.
>
>>so why does he write these essays? Why does he fill
>>them full of crap?
>
>are you saying that his account of the various hoaxes are lies?
You just mention one of the worst parts of his piece. What are these hoaxes
and what bearing do they have on the Neandertal example or human evolution as a
whole? He is just obfuscating the issue because he can do little else. This
is dishonest. Doesn't it even penetrate into your awareness that it was
scientists that uncovered these hoaxes or set the record straight on
misidentified fossils? Creationist had no part in this scientific endeavor.
You have to consider the evidence that we have, not the evidence that we do not
have or have discounted because they were hoaxes or misinterpretations of the
data. Whenever you see Piltdown as evidence against the fossil record in a
creationist piece you should throw it away. It is that simple. People that
are that lame can't be trusted to tell you anything of value. On some level
you know this, but you just can't accept it.
>
>>He only deceives people like yourself. He certainly
>>doesn't convince anyone that understands the data that he has something of
>>interest.
>>
>>You might be able to get dewy eyed and praise people like this, but I can't.
>
>I didn't ask you to. But at least don't demonize them, either.
>
>----
>zoe
So, it is OK to deceive people like yourself as long as you want to be
deceived.
Ron Okimoto
Robin Levett
news:3dbbec64....@news-server.cfl.rr.com...
<snip>
zoe; this refers to "nuclear" DNA.
<snip>
....of nuclear DNA...
> (no, not thousands).
....yes, thouands - of mtDNA.
"Nuclear" DNA.
> Quote:
> "Fortunately, from the FEW studies of nuclear DNA sequences, it is
> clear that what is called 'race,' although culturally important,
> reflects just a few continuous traits determined by a tiny fraction
of
> our genes." Pp. 1219, 1220.
>
> >I'd like to
> >find some, it wouldn't bother me a bit. We share some of our MHC
alleles with
> >chimps.
>
> and don't forget the mouse, with whom we "share" just as much.
Relevance, given what MHC alleles are?
>
> >Some of the variation in our genomes is very ancient. There is no
law
> >that says that we can't maintain such variation by just dumb luck
or by
> >selection. If our ancestors had this variation we could have this
variation.
> >It is that thing called common descent.
>
> this last, you must agree, is pure speculation, not science.
No.
>
> >If Neandertal sequences exist in the current population they would
have to be
> >very rare. It is very unlikely that the people that found and
preped the bones
> >all had someone with Neandertal DNA in the group. One group is a
possibility,
> >but all the research groups is not at all very likely.
>
> ALL the research groups -- meaning your three or four? That is too
> much weight given to a two-legged stool.
>
> >Neandertal like
> >sequences probably do not exist in the current human population.
>
> speculation, pure speculation.
>
> >If contamination were a problem why would only the Neandertal like
sequences be
> >recovered?
>
> because there might be many more Neanderthal sequences in the human
> population than we thought? Of course, that is pure speculation on
my
> part, also, for what it's worth.
Indeed. The difference is that so far Ron's speculation is founded
upon the evidence of thousands of sequences; yours is founded upon "we
might possibly find this if we just keep on looking".
....of "nuclear" DNA...
> are insufficient to come to a conclusion
> yet.
>
> > I haven't kept up with the research,
>
> you can say that again -- and yet you jump all over Sean?
>
> > but I'd bet the number of
> >extant human sequences number in the tens of thousand
>
> no, a mere 70.
....of "nuclear" DNA...
>
> > without finding a single
> >sequence like Neandertal, and these researchers have been looking
for
> >diversity. What you seem to be missing is that by sampling just
these few
> >thousand humans they have actually sampled hundreds of millions.
>
> Ron, you continue to build your theory on pure speculation. It is
not
> thousands. Back up.
zoe, you continue to sound confused. It is thousands.
>
> >If one of
> >your very distant cousins has been included in the testing and you
share some
> >great, great, great maternal grandmother, you have been sampled
too. All of
> >their extant maternal relatives have also been sampled. They
haven't just been
> >looking at some small inbred population, they have been covering
the globe to
> >get their samples. It is a possibility that we will find other
mitochondrial
> >types, but these types will be rare if they exist.
>
> well, here stands one witness, Ron Okimoto, who is testifying, not
> even by hearsay, but by "I think so-say." Of course, this is
familiar
> verbiage since a lot of evolutionary theory is couched in similar
> terms -- "It is a possibility"....
zoe, you do realise that here Ron is conceding that it is a
possibility that we may find Neanderthal sequences. If you wish to
dismiss that possibility,...
>
> >>>>> All existing Neanderthal sequences fall outside those limits.
> >>>>
> >>>>all four or five of them, right. I'm impressed by your
> >>>>four-person-high mountains of evidence.
> >>>
> >>>Considering the evidence that you have, it is a mountain, isn't
it?
> >>
> >>the evidence I have is the same evidence you have, except that you
> >>have chosen to draw what I would consider to be premature
conclusions,
> >>and I have chosen to leave the door wide open.
> >
> >You can't evaluate the evidence in a coherant fashion.
>
> I consider the Science journal to be very coherent.
....which referred to "nuclear" DNA sequences.
>
> >It is your bias that is
> >the problem and not mine or any other scientist.
>
> but, Ron, you are definitely biased towards the idea that thousands
of
> human sequences have been done. Do you think your bias is in the
way
> here?
http://www.hvrbase.org/Paper/hvhm.pdf
How many mtDNA sequences? Thousands.
zoe, the Neanderthal sequences in question are mtDNA sequences. There
is a very substantial difference between mitichiondrial and nuclear
DNA, and the number of nuclear DNA sequences and the number of
mitochondrial DNA sequences are not the same.
I've snipped the rest; it perpetuates the confusion you have
repeatedly exhibited above between the two types of DNA.
--
________________________________________________________________
Robin Levett
rle...@ibmrlevett.uklinux.net
(address munged by addition of Big Blue)
Atheist = knows of and uses Occam's Razor
Agnostic = knows of but isn't sure whether to use Occam's Razor
Fundy = what's Ockam's erasure?
___________________________________________________
Pokemoto
>Path:
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>
>
>
Snip:
>> I have to disagree, your writing are dishonest and misleading. You only
>have
>> to look at responses like Zoe's to figure that out. I've said to Zoe that
>I
>> think that what you are doing is vile and I meant it.
>
>Wow! "Vile"? Hmmm... It almost sounds as if you are defending
>evolution as some sort of moral position... a religion perhaps? You
>know Ron, I disagree with you strongly on many things that you say,
>but I do think that you honestly believe that what you say is true.
>Perhaps you should give me that same benefit of the doubt? I think
>that your statements are also misleading, but that you are not aware
>of this, because you honestly think that what you say is true. You
>may also think my statements are misleading according to your
>perspective, but at least you should consider that I might actually
>honestly believe what I am saying.
Science is amoral. I bring my own morals into the discussion. They are
separate from the science. I think that what you do is vile because you
continue to do it even when you must know by now that what you are doing
doesn't count for very much in the overall discussion. This has nothing to do
with the science except for the way that you misuse it.
>
>> >> Just read the papers on Neandertal DNA.
>> >
>> >I have read quite a few actually.
>>
>> You may have read them, but you obviously do not understand them.
>
>Obviously not. Of course, you must give me some credit for presenting
>my misguided thoughts to this forum for clarification since most of
>those that contribute to this forum strongly disagree with me. At
>least I don't hide under a rock somewhere and shelter myself by only
>talking with those who hold my same viewpoint.
No, but you keep presenting these bogus pieces and putting them up on your web
page.
>
Snip:
>>
>> So what, you are just admitting to obfuscating the issues.
>>
>> The decay rates don't matter if we actually find some DNA
>> to sequence does it?
>
>Actually, I think that understanding the relative fragility of DNA as
>well as its fairly rapid relative decay rate, is an important part of
>understanding why it is so hard to find Neandertal specimens with
>adequately preserved DNA. This issue also speaks to the fact that DNA
>finds, that claim to have found DNA in specimens supposed to be
>millions of years old, are highly questionable. This problem is not
>generally told to the public. That is why movies like Jurassic Park
>have contributed to the false impression that the public has as to the
>survivability of intact DNA.
And this has squat to do with the Neandertal sequences that have been
recovered. Other DNA sequence may be suspect, but you have to demonstrate that
this applies to the situation at hand. This is just another dishonest tactic.
Snip:
>>
>> You keep repeating this, but it is just wrong. There isn't a single human
>> sequence that is closer to Neandertal than it is to another human. You are
>> just looking a gross similarity. This is bogus and if you knew
>> anything about DNA sequence you would know that it is bogus.
>
>It seems to me Ron, that you have not carefully read the literature
>available. Consider some other replies to this particular discussion
>and you will note that the range for human variation is greater than
>the smallest difference between a modern human and the Neandertal
>sequence. That means that some humans match the Neandertal sequence
>more closely than they match certain other humans living today.
>(Krings, M., Geisert, H., Schmitz, R., Krainitzki, H., and Pääbo, S.
>DNA sequence of mitochondrial hypervariable region II from the
>Neandertal type specimen. Evolution, Proc. Natl. Acad. Sci. USA, Vol.
>96, pp. 5581-5585, May, 1999.)
I've read those papers and I understand them better than you do. The region
that they have sequenced is a known hypervariable region with known and
identified hotspots of mutation. These hotspots are known to change between
different mitochondrial lineages within extant humans. There is no reason to
think that these regions were more stable in the past. You really do not
understand how this analysis is done. Gross similarity doesn't mean much. You
have to overcome the fact that lineages can be established and that the human
sequences that are closest to Neandertal still map well within the nested
structure of the modern human population. It is that common descent thing that
you can't seem to wrap your brain around. Find out what a coelescent point is
and how we can infer sequence diversity back to that point. Then figure out
how you could be right if the colescent points say that you are wrong. There
is no extant human sequence that nests within the Neandertal sequences. They
are so distinct that this mistake cannot be made even with the small amount of
sequence that we have at this time. Gross similarity is just that, gross
similarity. We expect hotspots to collapse the difference between sequences
and we expect that just by chance the same mutations might occur in multiple
lineages. We can tell when this happens by looking at the sequence as a whole
and observing it in the context of the population of sequences.
>
>> Demonstrate that
>> what you claim is true. Find a modern human sequence that is closer to
>> Neandertal than it is to another extant human. You claim that they
>> exist, but only by using the wrong measure. Just because sequences differ
>by
>> the same number of substitutions doesn't mean that the substitutions are
>the
>> same. Even though two modern human sequences can differ by 24
>substitutions
>> they are different substitutions than the 22 that the closest human and
>> Neandertals differ by. These are three different individual modern humans.
>
>Are you saying that, depending on the type of substitution difference,
>individuals with wider separations can be more related than those with
>fewer total differences? If so, this is a far different theory than
>that proposed by every journal that has reported on this topic (At
>least the ones that I have come across). Perhaps you should write
>your own paper based on this hypothesis of yours. Personally, I think
>that it is weak. If you are correct, no one should be talking about
>absolute numbers at all, but strictly about the types or qualities of
>substitutions involved. For you, absolute numbers mean nothing? Very
>interesting take on the issue. At least it admits the problem with
>the use of absolute numbers. And that, in my book, is a step in the
>right direction.
You just do not understand anything about the subject or you wouldn't be making
these basic mistakes. It could be ignorance, but ignorance should be curable.
Why do you think that you can use gross similarity of sequence to give you an
accurate assessment of the data in terms of how closely related two sequence
are? There is not doubt that under conditions of say less than 10% divergence
the estimate based on similarity will often give you a decent estimate, but
that is usually. You are talking about a few odd sequences out of thousands.
We expect mutations to be random, why would we expect the entire distribution
of sequences to give a good estimate of relationship between two populations?
Even when the mutations skew the data we can still use the nesting to identify
what groups the sequences belong in and all the modern humans belong with
modern humans and all the Neandertals belong with Neandertals. Read the papers
and tell me that that is not what they concluded.
>
>
>> Your interpretation of the data is bogus. Get the sequences and look at
>them
>> yourself. None of them will be closer to Neandertal than they are to
>another
>> extant human being. If they are 24 substitutions from eachother they will
>> likely be more than 24 substitutions from Neandertal.
>
>You are wrong in this statement Ron. In fact, a more recent analysis
>shows that the variation range for humans is between 1 and 35. There
>are in fact humans living today, although rare, that are farther from
>some other humans living today than they are from Neandertal mtDNA
>sequences by a margin of 5 or 6 (Krings et al., 1999. above
>reference).
You are wrong. You are using the wrong measure. If you can't accept that,
there is nothing that I can do. It only reflects on your inadequate
understanding of the topic at hand. Think about what range and distribution
means. All of these human sequences still are derived from one that existed
sometime in the past. All Neandertals have a different common ancestral
sequence than all extant humans. You might honestly believe that you are onto
something, but it is only because you do not understand the conclusions of the
papers that you have read.
>
>> Not only that, but the
>> sequences will nest within modern humans and will not be found to be from
>the
>> Neandertal lineage.
>
>Nesting is a different issue entirely. Ethnic groups and even family
>groups also have nested DNA sequences, and yet they belong to the same
>species. Nesting, by itself, does not establish the existence of a
>new species.
It is not. Nesting is the only real measure worth talking about. You should
know this. You don't even know how nesting is used to establish differences
between species do you? Ethnic nesting doesn't mean squat when those sequence
nest within the larger population of sequences that we call humans. The thing
that is important about the nesting in Neandertal sequences is that they fall
at least 3 times the genetic distance outside of the extant human population.
This isn't just ethnic separation because all that diversity is already counted
within the extant human population. Neandertals fall outside of that nesting.
That is what makes the case for their being a different species. They are not
included within the variation found within our species.
>
>> You do know about common descent and nested similarity,
>> don't you? You are using a stupidly simple measure of difference and
>drawing
>> the incorrect conclusion from it.
>
>"Stupidly simple"? I am using the same measure of differences used by
>those who are publishing the data. If my measure is stupid, then,
>according to your statement, their measures are stupid as well... and
>that is my whole point.
No you are not. You are interpreting the data that they provided in an
incorrect manner and drawing unfounded conclusions from your incorrect
interpretations.
>
>Nesting is the minimum requirement to assume common decent. However,
>nesting does not PROVE common decent. Similar DNA nesting can be
>found in very different phenotypic creatures and very different
>nesting patterns can be found within different groups contained within
>the same species. Phylogenies based on genetic analysis and nesting
>patterns are not always intuitively clear.
Do the problem cases apply here? About the only time that nesting give
inconclusive results are when the populations are too closely related to make a
call or when two species diverged a long time ago and evolved in a star pattern
(they diverged in a short period of time on a geologic scale). I don't even
know of examples of some of the things that you are insinuating occur. Do you
have any references?
What we have here are two closely related populations that may be different
species. The sequence diversity is clear cut and the separation of the two
populations is clear. The only problem is that we have only 3 sequences from
one population, but we have thousands from the other. Even with this
limitation your interpretation amounts to nothing by clutching at straws
compared to the scientific inference from the data.
Snip:
>> So what? You are misinterpreting this data. It does not mean what you
>think
>> that it does. You are wrong and your analysis is bogus. You obviously
>> do not understand what you are talking about. We would not
>> class different ethnic groups as different species. Why would we?
>
>Exactly. Why would we?
Only someone equiped with your poor understanding of the data would confuse the
ethnic differences with the differences that we observe between Neandertal and
modern humans. Exactly, why would you even consider it a possiblity?
However, based in absolute differences, they
>are sometimes more different than the differences that exist between
>some of these groups and truly different species.
You can keep repeating this mantra, but it doesn't wash. You probably realize
it by now, but you can't admit it to yourself. Your argument seems to be based
on an incorrect interpretation of the data. You can't just keep saying it must
be this way because that seems reasonable when it is the wrong way to look at
the data and noone would make that mistake that wanted to honestly evaluate the
data.
Just think for a moment, why can all modern human sequences be found to nest
within modern humans even though they are by chance closer to Neandertal
sequences than they might be to some other human sequence. Each modern human
lineages have a different number of substitutions compared to another. We
expect variation in sequence and variation in gross similarity between
sequences, but the fact remains that they all have the same colescent point.
This point is not shared between the modern human and Neandertal sequences. I
can't make it any plainer. You are wrong and if you could evaluate the data
you would see this for yourself.
>
>> The sequences would still nest within humans and not outside
>> of humans no matter the gross differences between them.
>
>Again, this is not the assumption made by the authors writing up their
>conclusions on their own work. They make their conclusions based on
>the "gross differences", and not, as you suggest, on the exact type of
>differences found.
No they did not. What do you think that they based their divergence estimates
on? You are talking about the simplistic analysis that as a whole the
neandertals cluster differently than modern humans.
This is a no brainer, they cited examples of divergent modern human sequences,
but how do you think that the phylogeny was constructed. It wasn't constructed
on gross similarity. There wasn't a single modern human sequence that branched
with the Neandertal sequences. If what you claim is true at least one modern
human sequence would be found on the Neandertal branch. Why was this not the
case? Why was the colescent point placed at around 500,000 years for the
modern human and neandertal common ancestral sequence, and the colescent point
for modern humans is 75,000 to 150,000? How could your simplistic argument
mean anything when it didn't affect the placement of the sequences in the
phylogeny?
I was using the most recent estimates that I've seen. The Gibbons article
discussed data that has not been confirmed in the last 4 years. You shouldn't
rely on creationist literature for your science information. Look it up
yourself, find the articles in question and verify that the high rate of
mutation was never confirmed. It is considered to be higher than it once was,
but not a rate that would make 10,000 years possible. This is how science
works: someone makes an interesting observation. This one went counter to many
expectations so it was immediately tested by many labs. They couldn't confirm
those observations. The original scientist would be famous by now if their
data had been confirmed.
>
>Besides this problem, it seems to me that the "corrections" made in
>the calculations of divergent dates are not primarily used to support
>the hypothesis that Neandertals belong to a different species. The
>reason given for this is that the "corrections" do not change the
>"general situation." In other words, the absolute range of
>substitutions differences remains approximately the same. The paper
>strongly urges that the absolute average differences between
>Neandertals and modern humans speaks in favor of the hypothesis that
>Neandertals are in fact separate species.
>
>Now, I will agree that the evidence speaks to the common decent of
>Neandertals from a different starting point than seems to be the case
>for most humans living today. However, the same conclusions can be
>drawn for the common decent of various families and ethnic groups
>living today. These differences however, cannot be used to prove or
>give evidence for species separation. I do not think that these
>clustered variations and similarities that occur within a single
>segment of DNA can be used as evidence of unique or separate species
>boundaries since many of these same differences, to the same degree,
>can be seen within single species groups living today.
No, demonstrate that Neandertals fall within known ethnic diversity. They do
not. It is that simple.
>
>
>> >> They are
>> >> related to us, they fall between modern humans and chimps.
>
>Obviously I agree that Neandertals are related to us. It is my
>position that they are only an ethnic variation of Homo sapiens. Now,
>even among evolutionists, I would say that you are on your own when
>you say that Neandertals "fall between modern humans and chimps."
>Neandertals are no closer related to chimps than humans are as far as
>their mtDNA sequences are concerned, even given the "corrective"
>changes described above. They are in fact, "approximately equidistant"
>as far as their mtDNA substitution differences are concerned... if not
>a bit farther since certain humans are more similar to chimp mtDNA
>than the Neandertal mtDNA is.
We are looking at a very short sequence and you are dealing with site
saturation when you look at chimps and humans. Chimps don't even make a good
outgroup for this sequences. The probability is that if a site is different
between humans and chimps that it has been hit more than once by a mutation.
This is where your gross similarity goes drastically wrong. The chimp data
indicates that you don't have a valid point. It doesn't support you.
Snip:
>> Idiot. This is beneath even you. If the sequences fell where you say, why
>> would modern humans be 500,000 years distant from the Neandertal type
>common
>> ancestor and 5-8 million from the chimp human ancestor.
>>
>> By anyones measure this is between modern humans (75,000 to 150,000) and
>> chimps.
>
>You aren't just calling me an idiot; you are calling Pääbo and his
>team idiots. Check out page 3 of the reference cited above. You will
>find there a comparison table that cross-matches humans, Neandertals
>and chimps/bonobos. You will note from this table that Neandertals
>are no closer to chimps/bonobos than modern humans are, despite the
>"corrections" used to obtain this data. In fact, you will find that
>there are some humans that are closer matches to chimps/bonobos than
>is the most closely matched Neandertal sequence. The closest human
>match shows "78" differences while the most closely matched Neandertal
>sequence shows "84" differences.
Again this is just gross similarity and we expect Neandertals to be the same
distance minus 30,000 years from chimps as humans. It is the nesting of the
sequences that is important. Just think about it for a few minutes. We expect
just as much sequence evolution in Neandertals as modern humans since the
common ancestor with chimps and humans. This is an expectation that is
confirmed by this table. The exact nature of the sequence is the important
data for any further analysis. Neandertals nest at 500,000 years with modern
humans and chimps nest at 5-8 million years. You don't get this from gross
similarity.
>
>By the way, as an educated professional, as I assume that you are a
>professional, even if I were an idiot as you say, it is not
>professional to call an idiot, an idiot... at least not in public. It
>reflects more on you than it does on the idiot.
Possibly, but when you act like an idiot people tend to call you an idiot. We
wouldn't have the word if we couldn't use it to accurately describe someone
else. Think about the table data, think about the nesting, and then consider
the term idiot.
Snip:
>> What a waste of a brain. You must realize your error by now. Just
>> think about it for 5 minutes. You are wrong about this, and I
>> can't understand how you could be this wrong.
>
>Actually, despite my thinking about it for hours on end, I have not
>realized my error as of yet. In fact, I truly do not understand how
>you can maintain your position. Your arguments even seem to contradict
>the standard attempts to explain this data in support of the separate
>species status of Neandertals. The standard arguments attempt to show
>that the absolute number of substitution differences along with the
>average clustering of these differences indicate that Neandertals not
>only came from a different common ancestor than most humans but that
>Neandertals should also be classed as a different species altogether.
>This argument fails because individual ethnic groups living today have
>unique genetic differences that are different from every other ethnic
>group of humans living today.
Ethnic groups don't wash in this instance because Neandertals are not just
another ethnic group. They fall outside of all known groups of modern humans,
but all modern humans can be grouped in the same group. That is what is wrong
with this argument. It just isn't what you think.
SNip:
>So, it is my position that a single characteristic cannot be
>adequately relied upon to determine species boundaries. That is all.
>I think it is an error to propose such a thing as has been done with
>Neandertal mtDNA. Its superficial reasonableness makes it very
>appealing and therefore one can easily be misled by it, but a more
>careful investigation will show the limits of such hypotheses.
Sure it is reasonable to take that tack, but you know that you are probably
wrong in this case. That is the important thing to acknowledge. You are just
grasping at air. If you were honest with yourself you would admit that there
could be a problem, but all the other data on human evolution tells you that
this is just another point that should tell you that you are wrong. No one
says that the Neandertal data stands by itself. It is only one piece of the
body of knowledge about human evolution. The sum of the whole is what you
can't explain.
Snip:
>> I wish you weren't serious about this post. It makes you look moronic, but
>> that is how you actually are. Getting through medical school doesn't
>> make you intellectually honest. It isn't my fault that you chose to
>> use your ability to lie to people, and confuse people like Zoe.
>>
>> It could be that you are just ignorant or stupid, but I don't believe that.
>
>I am fully aware that I look moronic to those such as yourself. You
>must give me credit though for asking such idiotic questions even
>though I will be called "idiot", "crazy", "liar", and much worse
>actually, when in fact I am honest in my questions. If I am confused,
>I am honestly confused.
>
>> Ron Okimoto
>
>Sean
Honest confusion is one thing. Putting up crap on your web page is another.
Don't you have any compuction of trying to avoid deception. Why do you believe
the creationist crap and put ridiculous things like Piltdown in your efforts?
This doesn't reflect very much of an honest intent to me. It looks like a
purposeful ruse. You don't seem to be any better than the guys that you
immulate.
Ron Okimoto
Frank J
> For those interested in pictures and references etc., I discuss
> Neanderthals and other "early hominids" further at:
>
> http://naturalselection.0catch.com/Files/Early%20Man.html
And you put Piltdown Man first??? I guess if you taught physics you'd
start with cold fusion.
Cyde Weys
"Jon Fleming" <jo...@fleming-nospam.com> wrote in message
news:agtnru8unfli4pslg...@4ax.com...
You show 'em! I'd love to see what response they have up their sleeve now
....
Pokemoto
>Path:
ews.ems.psu.edu!newsfeed.stanford.edu!darwin.ediacara.org!there.is.no.cabal
>From: dina....@snet.net (Don1)
>Newsgroups: talk.origins
>Date: Sun, 27 Oct 2002 16:05:38 +0000 Snip:
>A criticism of overlapping ranges is a fair statistical criticism,
>especially since somewhere there is an N=1. However, maybe the
>doctor is confused about what the ranges mean? I know that I am.
>Some details about these numbers are certainly left out. Could
>someone clarify this point?
>
>
>Thanks,
>Don
The gross similarities doesn't mean as much as the actual sequence. Chimps are
expected to have accumulated just as many substitutions since the common
ancestor as Humans. Neandertals would be expected to have accumulated just as
many substitutions as modern humans minus around 30,000 years worth (the time
since they went extinct and stopped evolving). We don't expect all lineages to
evolve at the same rate, just by chance some may have more mutations than
another. We are only looking at a few hundred base-pairs. Mitochondrial DNA
has the added limitation in that transitions outnumber transversions by at
least 10:1 and probably over 50:1 in the D-loop region. This just means that
on a first approximation that there are really only two states possible at each
position instead of four. This limits the information content of the sequence,
and makes possible convergence by chance even more likely.
In the case of Neandertals the sequences are close enough so that our estimates
can be fairly accurate, and we have the added bonus that the three Neandertal
sequences are about as closely related to each other as the most divergent
human sequences are. This just means that even though the estimate for the
common ancestor with Neandertals and modern humans is half a million years, all
the Neandertal sequences are more closely related than that.
This just means that at about the same time in the past (around 100,000 years
ago) there was a mitochondrial Eve for Neandertals and modern humans, but they
were very different mitochondrial sequences because around 400,000 years of
evolution had occurred between them before those single mitochondrial types
took over their respective populations. This just means that the Neandertal
and modern humans mitochondrial types have a significantly different coelescent
sequence. All extant modern humans share a common evolution of 400,000 years
worth of mutations that are not shared with the Neandertal sequences.
Just because a few modern human and Neandertal sequences have converged by
chance after their respective coelescent sequence we can still tell that all
modern humans have the basal modern human mitochondrial sequence and not the
basal Neandertal sequence. This can be done until mutations obliterate the
informative sites between Neandertals and modern humans. This wouldn't have
happened to a significant extent for another million years or so of evolution
along the lineage of Modern humans. The important thing to note is that even
though it would become a problem a few million years in the future, it is not a
problem now.
Ron Okimoto
zoe_althrop
wrote:
snip>
>Zoe, it is amazing the mental gymnastics that you will go though
>to avoid the isochron. It would take trillions of years
>for all the parent isotope to have all decayed if we are using
>Rb-Sr (49 billion year half-life), Sm-Nd (106 billion year half-life),
>Lu-Hf (36 billion year half-life), or Re-Os (43 billion year half-life).
this has been a hypothetical discussion, as far as I'm concerned, to
test the definitions of the isochron. If the isochron's definitions
cannot theoretically stand up to the test of time, if its intercept
will change with the sufficient passage of time, then the
identification of the Y-intercept has to be in error, is how I see it.
>You appear to be imagining the trajectory of a single point without
>calculation where all the other points will be at the same time.
no, I said, "...the trajectories (plural) of the other samples will
have their intercept correspond to the approximate intercept of the
exhausted-P sample." I am not concentrating on the trajectory of a
single point.
>By the time that enough time has passed to drive one of those points that
>was not initially by the y-intercept to being on the y-intercept (within
>measurement errors) the entire isochron will have a very high slope and
>thus the entire isochron will be close to the y-intercept. The result
>of such a test is likely to be "infinite" age.
not yet. Infinite would be when all samples end up in the
unmeasurable P region and appear to be zero. The height of the slope
is not being addressed here, but the fact that if the intercept
APPEARS to change (due to instrumental failings) then it cannot
therefore be identified as oldD/Di.
>Here is some homework for you.
>
>Let us imagine the following diagram.
>
> |
> |
> |
> |
> |
> |
> a'
> |
> | a b c d e
> |
> |
> |__________________________
>
>
>a, b, c, d, and e are the points at time zero.
>
>a' is where a will be in the far distant future (of time zero).
>(It might be actually lower or higher up on the y-axis since
>the exact location where a's tragectory will hit the y-axis will
>have to be calculated.)
>
>The your homework problem is to figure out where b', c', d',
>and e' are.
without actual numbers (hey, that's my speed), I can only give you an
approximation of what I think it should look like. Here is how I
would expect the isochron to look at the point where sample A moves
into zero territory.
|
|
| e
| d
| c
| b
a'
|
|
|
|
|__________________________
sample A will be a little off, yes, but as long as it has been within
acceptable scatter along with the other samples, it should still fall
within the acceptable scatter for the other samples.
> Plot those points and see what the isochron looks
>like. What kind of date would the isochron method give?
very old date, but that is not the issue here. The issue is, will the
identification of the isochron's intercept hold up as oldD/Di, after,
say 500 billion years? If it doesn't, then the identification of the
Y-intercept is incorrect.
>Remember
>the the higher the slope the higher the age. And then what if there
>is scatter?
small scatter is acceptable. And it does serve to hide the small jump
of Sample A from its original trajectory.
>If the points are scattering over the y-axis then the
>"age" given by the method will by infinite which is nothing more than
>saying older than what are equipment and methods can measure.
why should scattering give an infinite age? Only one point jumps off
course at the Y-intercept, but it remains within acceptable scatter,
and the other samples continue to remain within the original
acceptable scatter, also.
>You can make up your own numbers if you like. But if you want numbers,
>say that we are doing Rb-Sr, that Sr-87/Sr-86 is 0.7 for a through e,
>and that the Rb-87/Sr-86 values of a through e are 0.1, 0.2, 0.3, 0.4.
>and 0.5 respectively.
no, let the above hypothetical isochron suffice for illustrating my
point -- that the Y-intercept will change with the passage of time,
therefore the Y-intercept cannot be oldD/Di, since oldD/Di doesn't
change.
>[snip]
>> I think there is plenty room for sampling error when just three or
>> four Neanderthal mtDNA sequences have been examined against a mere 70
>> individuals worldwide. See Science, 16 February, 2001, under the
>> illustration titled "The global family." This is an article by Svante
>> Paabo. Quote: "A network illustrating the relatedness of a series of
>> DNA sequences within a 10,000-base pair segment of the human X
>> chromosome samples from 70 --" (70!!) -- "individuals worldwide." p.
>> 1220.
>[snip]
>
>I am looking at the original paper in _Cell_ that first announced the
>Neandertal mtDNA.
after reading further, I see my mistake -- that one type of test deals
with mtDNA and the other (in Science) deals with nuclear DNA.
But my point still holds. The data is insufficient, imo, to come to
hard and fast conclusions -- certainly not yet, anyway.
>They compared the Neandertal sequence to
>"994 contemporary human mitochondrial lineages, i.e. distinct
>sequences occuring in one or more individuals, found in
>478 Africans, 510 Europeans, 494 Asians, 167 Native Americans,
>and 20 individuals from Australia and Oceania..."
>
>In short you are completely wrong that only 70 human were compared.
>The number for the 1997 paper was, adding them up from above, 1669
>individual people representing 994 distinct sequences.
true, you are right on the numbers there, but I would still look for a
much larger sampling universe, and certainly not so much disparity in
numbers between the two groups. Three Neandertal lineages to 1,669
contemporary human lineages seems terribly unbalanced to me. Not only
that, but I notice that of 16,569 base points, only 333 were examined.
Is this sufficient upon which to rest your whole unwieldy theory?
>And even if it was just 70, your case would still be weak. Do you
>think that by chance they picked just freek individuals to sequence?
>The odds of that happing are almost impossibly low.
no, I don't think they picked freak individuals to sequence. But I
would think that you would need more than three Neandertal sequences
in order to determine if there might be some that fall within the
range of human sequences. And, vice versa, you would need way more
than a thousand modern sequences in order to determine if any
Neandertal sequences might still be around -- dead or dying breed that
they might be.
>In any even lets go back to the data from the original _Cell_ paper.
>
>When comparing the differences between the 994 human lineages,
>they found they an average of 8.0+/-3.1 differences with the
>range being from 1 to 24. (And if they compared people the
>range would obviously been from 0 to 24. Doing the same
>between the human lineages and the Neandertal gave
>27.2+/-2.2 with a range of 22 to 36.
>
>Now you will say that they overlap. True, but that does not make
>Neandertals in modern humans.
wait a minute. I don't think I've ever said that Neandertals are
modern humans. The mere fact that they existed before our time is
sufficient to put them into pre-modern classification. But that does
not mean they are a new species. I would identify them as simply a
dying or dead segment of humanity.
>First of all let notice just how
>rare it was for the human-human comparison were larger than human-
>Neandertal comparisons.
>
> "In total, 0.002% of the pairwise comparisons between human mtDNA
> sequences were larger than the smallest difference between the
> Neandertal and a human."
>
>Second, the difference between the Neandertal and the African,
>Asian, American, and Australian/Oceanic lineages were approximately
>the same, just as what you would expect if Neandertals and modern
>humans made up distinct populations of individuals.
maybe so. BUT three sequences is NOT enough. Not to satisfy me,
anyway, and hey, I'm people, too.
>And as has been pointed out by others, it is not just the
>absolute number of differences that counts. What the actual
>differences are is very important too. This brings up the need
>for a phylogenetic analysis.
>
>To be able to use data from 16 chimpanzee lineages the number of human
>lineages was reduced to 986. Then the 16 chimp lineages, the Neandertal,
one? We're down to ONE now?
>and the 986 human sequences were used for a phylogenetic analysis. The
>chimp lineages were used to root the tree -- in other words it was
>assumed that chimps are distinct from the human/Neanderal group.
>The result was was that Neandertals are distinct from humans.
one Neandertal differed from the chimps and the modern humans, and
this was considered conclusive? The theory of evolution teeters on
the head of a pin.
>And I don't think I have to mention that since the 1997 paper _Cell_
>paper the data set that one can use has grown: the original authors
>sequences another mtDNA sequence from the same individual and other
>groups have sequenced other Neandertals.
how many Neandertals?
>And more sequencing of
>humans, chimps, and other primates has occured as well. And yet
>the conclusion has only become stronger.
you're getting vague on me now.
>The publication of the second Neandertal individual is at
>http://www.nature.com/cgi-
>taf/DynaPage.taf?file=/nature/journal/v404/n6777/full/404490a0_fs.html
>
>In particular the results of their phylogenetic analysis can be seen
>in the diagram at
>http://www.nature.com/nature/journal/v404/n6777/fig_tab/404490a0_F3.html
>
>Notice that 5846 modern humans were used in this study representing
>1,897 distinct sequences. The Neandertal mtDNA is still quite
>distinct from humans mtDNA.
but you're still down there at two Neandertal sequences. What good is
that?
>Also of interest is http://www.pnas.org/cgi/content/full/96/9/5077
>which shows just how undiverse humans are compared to other
>hominoids (i.e. apes). "Several chimpanzee and bonobo clades
>(and even single social groups) have retained substantially
>more mitochondrial variation than is seen in the entire human
>species." This is very inconsistent with YEC dogma that
>Pitman, AiG, ICR, and others would have us believe.
I don't know, but scientists must take laypersons for fools after all.
They make these sweeping statements on the barest whiff of data. For
instance, they start out with: (caps mine)
"In spite of the ABSENCE of relevant fossils, studies of genetic
variation have SETTLED the question of whether humans are more closely
related to gorillas or chimpanzees in favor of the latter (1).
However, most such comparative studies have been based on NO MORE THAN
SIX INDIVIDUALS of each taxon with the exception of humans."
And you expect me to be impressed already with this kind of beginning?
And then you point out this statement:(caps mine)
"Several chimpanzee and bonobo clades (and even single social groups)
have retained substantially more mitochondrial variation than is seen
in the ENTIRE human species."
as if the entire human species has been checked. Come onnnn, now.
----
zoe
zoe_althrop
wrote:
snip>
zoe wrote:
>>consider the variation that develops instantly from intermarriages.
>>There is no such thing as a true race, and intermarriages confirm
>>this. I think you know this already and are just testing me, right?
>
>This has virtually nothing to do with the argument at hand. Why did you even
>bring it up?
the reason I brought it up is because you said that variation in
extant humans is a large problem for those who think that everyone was
created a few thousand years ago. My answer is that variation in
sequences can occur rapidly -- just observe the morphing of races
through intermarriage.
From what I am reading here (hastily at that), DNA sequence variation
is a result of single nucleotide polymorphisms, and though
evolutionists like to consider that these variations reflect past
mutations, I would interpret them to mean, instead, that humans have
been programmed with the ability to vary widely in the space of a
generation of two. I mean, there are a LOT of SNPs in evidence. A
quote from Nature:
"...comparing two human DNA sequences results in a SNP (single
nucleotide polymorphism) every 1,000-2,000 nucleotides. That may not
sound like much until you realize that there are 3.2 billion
nucleotides in the human genome, which translates into 1.6 million-3.2
million SNPs. And that's just from comparing two sequences -- the
total number of SNPs in humans is obviously much more." Nature, Vol.
409,15 February, 2001, p. 821
With that kind of programmed capability from the start, the human race
can quickly go from a now-extinct Neandertal human to an extant modern
human -- in a matter of a few thousand years.
>Eve had a single mitochondrial type. Demonstrate that she did not. All extant
>humans are descended from Eve using your model. Where was all this variation
>pre programed in?
and how have you determined Eve's mitochondrial type?
>All Eve's daughters and sons inherited her mitochondrial mitochondrial type.
>This would have been the same one as Adam's because she was essentially a clone
>made from Adams rib.
sounds to me like you were present, taking notes at the creation of
the first human. How do you know exactly what was and was not
inherited? You'd have to know exactly the richness of the genetic
makeup of the first humans in order to form the conclusions you do.
>>>>>Are Neandertals human?
>>>>
>>>>I would guess yes -- a different species of human, but still human. I
>>>>mean, just recently, I saw a taxi driver, a living, breathing human
>>>>taxi driver, whose cranium was shaped like some of those early
>>>>drawings of ancient hominids -- the brow projected far out above the
>>>>eyes, hung low, and sloped back, with very little forehead in
>>>>evidence. If he were to die and be found a few years from now, he
>>>>would probably be considered some kind of missing link. Yet there he
>>>>was, driving a car and acting like any other normal human being.
>>>
>>>You have some weird concept of sampling error.
>>
>>I think there is plenty room for sampling error when just three or
>>four Neanderthal mtDNA sequences have been examined against a mere 70
>>individuals worldwide. See Science, 16 February, 2001, under the
>>illustration titled "The global family." This is an article by Svante
>>Paabo. Quote: "A network illustrating the relatedness of a series of
>>DNA sequences within a 10,000-base pair segment of the human X
>>chromosome samples from 70 --" (70!!) -- "individuals worldwide." p.
>>1220.
>
>This is a totally different study on sex-linked DNA sequence of the X
>chromosome. Do you realize that mitochondrial DNA is cytoplasmic and
>maternally inherited.
after reading a little more, I realize that now. My point still
stands, though.
>Do you realize that thousands and thousands of
>mitochondrial sequences have been and are being sequenced.
last I counted in the links provided, I got a little over 2,000, not
thousands and thousands.
>It is a lot of work
>sequencing 10,000 bp from 70 individuals, but the study is testing something
>else, not what you think.
>
>What you have to ask yourself is why these different studies on different DNA
>sequence tell us a consistent story about human evolution?
consistent over a universe of three Neandertals? It's just not enough
to convince me.
>The X chromosome is not maternally inherited. Females get one copy from their
>fathers and one copy from their mothers.
say that again? If the X chromosome is not maternally inherited, why
would you say that females get one copy from their mothers?
>>> What type of modern human is
>>>the most likely to fossilize today?
>>
>>those swept away by some flood, maybe, including our taxi-driver
>>Neanderthal friend.
>
>I said most likely. What was the most likely type to be preserved in the flood
>victims?
there is no likely type. Floods have no preference.
>>
>>>These aren't
>>>just funny looking modern humans or we would find modern humans mixed in
>>with
>>>them.
>>
>>how is it possible to find modern humans mixed in with humans from a
>>past era? Modern humans are stuck in today's setting. It would be a
>>shock to find modern humans alongside human races from any other era.
>>This is common sense, not science.
>
>That is all modern science claims, but YEC claims something different doesn't
>it?
I don't know what YEC claims are. I personally would not expect to
find modern man mixed in with older human races. Modern belongs to
modern. But that does not mean that older human races are a different
species, just because modern man is absent. If there were giants in
"those days" then I would expect that humans were once larger, better
built, even more varied in genetic makeup due to environment, diet,
lifestyle (all of which have an effect on genes), but those
differences do not make them a different species.
>So you admit that the current scientific explanation is reasonable and backed
>up by the current findings, but YEC claims seem to be left out in the cold?
what are YEC claims? And if you want to classify variation as
evolution, then I could go with that. But variation has always been
demonstrated to be within limits, and the concept that a species can
vary its way outside of its bounds and become some entirely new
species (to wit: dinosaurs to birds, or chimps to humans) -- that is
fantasizing, imo.
>>>>>Are they some other creation?
>>>>
>>>>probably a result of inbreeding so that certain features and
>>>>characteristics became more pronounced.
>>>
>>>I assume that your evidence for this is with your evidence for your other
>>>assertions of similar value.
>>
>>I guess I'm going to have to pull out my Anatomy and Physiology next
>>and quote from the chapter on genetics?
>
>No just pointing out that you have as much evidence for this assertion and any
>others. It doesn't matter what you can dig up in some genetics text, but how
>you are applying it. Inbreeding will not cause the genetic variation that is
>observed in the Neandertals compared to modern humans. In fact it would seem
>not to be inbreeding because the Neandertal sequence that we have analyzed are
>about as far from each other as the most divergent modern human sequences are
>from each other. These guys don't seem to be very closely related by
>inbreeding. You might be better off suggesting that they were all selected
>under similar environmental conditions for their genetic morphology.
that is one way to look at it, but not the only way.
>
>>
>>>>>Why aren't they mentioned in the Bible?
>>>>
>>>>the Bible is written for other purposes than science, but it does
>>>>mention that there were giants in those days, some called Nephilim,
>>>>others Rephaim, and so on.
>>>
>>>You have a pretty low opinion of the gods of the Bible if you think that
>>>Neandertals are the half gods.
>>
>>there are many gods, false gods, and the Bible recognizes them as
>>such. But there is only one true God, the Creator of the Heavens and
>>the Earth.
>>
>>But, at any rate, why do you consider the Nephilim to be gods? They
>>were merely a superior race descended from giants in the earlier part
>>of Earth's history.
>
>I said that they were the half gods. Reread what I wrote. They were supposed
>to be the heros of old that were descended from the gods that mated with human
>females.
oh, okay. But that bit of info did not come from the Bible.
>
>It doesn't matter if they don't quailfy as "true" gods by your definition they
>were called gods in the Bible.
not the Nephilim and Rephaim. Do you want to quote where they were
called gods?
>Snip:
>
>>and what is your source for this number? Please give it to me so I
>>can see how it stands up against Paabo's statement that only a few
>>studies of nuclear DNA sequences have been done. Quote:
>>"Fortunately, from the FEW studies of nuclear DNA sequences, it is
>>clear that what is called 'race,' although culturally important,
>>reflects just a few continuous traits determined by a tiny fraction of
>>our genes." Pp. 1219, 1220.
>
>So what? We knew this 30 years ago using blood typing. Racial differences do
>not have much of a genetic basis. This just means that we are all more closely
>related to each other than some people want to believe. It says nothing about
>why Neandertals fall so far outside this variation that we can't group them
>within any of the known races.
again, a couple thousand versus two or three is not a big enough
sampling universe to come to any serious conclusions. Why do you ask
such a tall order of me? Until there is more evidence, I see no
reason to say that the matter is settled.
>
>Again, this is not a mitochondrial study. You are looking at the wrong
>experiment.
right. I missed the nuclear DNA part and tied it to mtDNA. Sloppy of
me...as usual.
>>>I'd like to
>>>find some, it wouldn't bother me a bit. We share some of our MHC alleles
>>with
>>>chimps.
>>
>>and don't forget the mouse, with whom we "share" just as much.
>
>As far as I know we share no MHC alleles with mice except the ones that have
>been genetically engineered to have human MHC for tissue transplantation
>experiments.
for the most part, from what I'm reading, we, as humans, share no MHC
alleles with each other, either. That is why rejection of grafts is
so prevalent.
> Our common ancestor with mice is so distant that we have no
>alleles in common, but we still share alleles with chimps.
not if you go by tissue rejection. The Major Histocompatibility
Complex prevents humans from accepting transplants from chimps and
vice versa. Maybe with abundant use of cyclosporins or other
anti-rejection drugs, you might be able to force a fit, but it is not
natural.
snip>
>What do you need? It is you that are being unreasonable and you know it.
>Where are these extant Neandertal sequences? Why haven't we found them? None
>of the researchers involved had Neandertal sequence or they would have stated
>this. Why would Neandertal sequence be the contaminant? Why wouldn't the
>researchers own DNA be the contaminant? In at least two of the studies they
>sent samples to an independent laboratory and the two labs got the same
>sequence from the same sample. You don't have a leg to stand on in this case,
>but you can't admit it. There is nothing that will satisfy you. Explain their
>results. Where did the contamination come from and why is the contamination
>always Neandertal sequence when they are working with Neandertal bones, but
>when they work with other human remains the sequences are not Neandertal? Even
>you should be able to reason through this one.
you are still using sweeping terms in reference to two or three
sequences. And now you're talking as if there is such an abundance of
samples that they can shoot off samples to independent laboratories
and they get the same sequence. Exactly how much of this precious,
easily destroyed mtDNA do they really have from their two-three
Neandertals?
>
>>
>>>Neandertal like
>>>sequences probably do not exist in the current human population.
>>
>>speculation, pure speculation.
>
>I have more evidence for this than you have that they still exist. Like I said
>I would like to see this variation in the extant population. The fact is that
>from the samples that we have taken from all the diverse populations it is
>unlikely that we will find a sequence as divergent as the Neandertal in the
>extant population of humans.
actually, it matters not one whit because, to me, it makes sense that
humans can vary as widely as Neandertal types, Nephilim types, Rephaim
types, modern-day types, and yet they remain humans. I'm beginning to
think that whenever you evolutionists see a variation in species, you
term that variation a new species. Am I correct? If so, then, yes,
there is evolution. But the rest of your theory boils down to an
unwarranted leap into space, with the earnest hope of jumping further
into space by using that last leap into the air as the basis for the
next jump.
snip>
>You aren't talking about the same study.
true. I take that back, even as I contend that it makes no difference
in what I am saying.
>Even the first Mitochondrial Eve
>paper had sampled around 150 sequences and that was back in what, 1987? We
>have thousands and thousands of mitochondrial D-loop sequences.
thousands of D-loop sequences is not the same as sampling thousands of
human lineages.
snip>
>Demonstrate that I am wrong. It is a possibility, no one would deny that, but
>it isn't a very good possiblity or we would have found these sequences already.
>
>In more than 16 years of searching why haven't we found at least one, when the
>purpose of most of the studies was to sample population variation? The studies
>have sampled isolated populations from Tibet to amazon villages to Kung bushmen
>in Africa. Where are the Neandertal sequences? Why are they so hard to find
>if they are such a rich source of contamination?
16 years of different types of studies, yes, but not 16 years of
searching for Neandertal mtDNA in humans.
snip rest -- sleep calls>
----
zoe
Sean Pitman M.D.
Let me pose a scenario for you, since you are into hypotheticals and I
also like hypotheticals for use as tools for asking questions and
explaining problems.
Consider the three different series:
1) AAAAAAAAAA
2) TAAAAAAAAA
3) CAAAAAAAAA
All of these series are different from each other by one substitution.
So, which one is related to any of the other ones to the exclusion of
the third one?
Lets make it more complicated:
1) AAAAAAAAAA
2) TTTAAAAAAA
3) CCCAAAAAAA
Again, with three differences each. Which two belong together?
1) AAAAAAAAAAA
2) AAAAAAAATTT
3) AAACCCAAAAA
Now, the differences involve different locations. Which two belong
together?
Ok, according to Krings et al., humans have a range of substitution
differences from 1 to 35. The closest distance between human and
Neandertal sequencing is 29. It is possible therefore to find two
humans that have more differences in their mtDNA sequences than exist
between one (or both) of these humans and the Neandertal sequence. In
other words, a given modern human might be 35 substitutions different
from his neighbor, but only 29 substitutions different from our
Neandertal friend. Am I getting it right so far?
Your point then is that this span of 35 differences is not as
significant as a span of only 29 differences because of a pattern of
differences in the 35 substitution span that is more consistent with
one group than it is with the different pattern contained in the 29
substitution span? In other words, you are saying that fewer
differences can actually be interpreted, based on certain patterns, as
a bigger difference than the absolute distance suggests?
Please, I agree that Neandertals appear to have separated from a
common ancestor with modern humans a while back, but I do not
understand how this can be calculated as anything farther back than
those two modern humans who are separated by a gap that is larger.
Perhaps you could explain this to me?
Lets take two humans who have identical mtDNA. The odds are that they
have a rather recent common ancestor... right? Now take two humans
who have 1 difference in a given region of mtDNA. The odds are that
they also have a recent common ancestor, but not as recent as those
who are identical... right? We can keep going with this to those
humans who have 10 differences, and 20. With each step, the
assumption is that the number of generations that these two
individuals are from a common ancestor increases by some number. But,
by the time you get to 10 substitutions, one might be able to pick out
some sort of pattern.
Looking at substitutions alone, lets say that I find 5 humans who are
separated from 5 other humans by 10 substitutions. Lets say that all
10 substitutions, in both sets of humans, affect the same nucleic
acids in a series of 500. One of the groups must be chosen at random
to be the substitution group (SG). Lets say that the substitutions in
the SG group read:
AAAAAAAAAA
Lets also say that these same positions in the non-substitution group
(NSG) read:
TTTTTTTTTT
We might conclude then that each of the two groups of five humans had
identical mtDNA within their individual group of 5 and thus are very
closely related to each other (ie: All five members of SG group are
closely related as are the five members of NSG group). However, time
of split from the common ancestor between the two groups must still be
calculated using the same method based on the absolute number of
differences between the two groups. It might seem very strange that
the two groups are separated by substitutions involving the exact same
locations. But, does this similarity in the specific location of the
substitutions indicate a closer relationship than if the locations
were different between individuals from the two different groups? In
one way it does. It means that those within a given group are closely
related, but it does not mean that the two groups are any more closely
related. For example, lets say that we have a family with five
children. Since mitochondria are always handed down from mother to
child (ie: no mixing occurs with paternal mitochondria), it is very
likely that all five children will have identical mitochondrial DNA
sequences. Lets say that right next door is another family that also
has five children. All of those five children will also most likely
have identical mitochondrial DNA. However, the two different sets of
five children will probably have some differences when compared with
each other especially if their parents belong to different ethnic
groups.
Lets say now that a third group (TG) of five comes along that has a
10-substitution difference from the SG group. Lets say that the
substitutions between the TG group and the SG group affect entirely
different locations than are affected between the SG group and the NSG
group. Obviously then, the locations that are different between the
TG group and the SG group would be identical between the SG group and
the NSG group. Follow so far? Lets say then that at the locations
that are different between the TG group and the SG group, that the SG
group reads like so:
TTTTTTTTTT
At these specific locations however, the TG group reads:
CCCCCCCCCC
At this point, the TG group is different from both the SG and the NSG
groups by at least 10 substitutions. But, what about the locations
that are different between the SG and NSG groups? What sequence does
the TG group have at these locations? Lets say that at these
locations the TG group reads:
AAAAAAAAAA
Of course, this would make the TG group identical to the SG group at
this location. So, the TG group is different from the SG group by
only 10 substitutions, but the TG group is different from the NSG
group by 20 substitutions. Make sense?
Common Ancestor
/| \
/ | \
/ | \
/ | \
/ | \
TG ------ 10 subs ------ SG -------- 10 subs -------- NSG
< -------------------- 20 subs ---------------------- >
OR – To visualize it another way:
AAAAAAAAAA
|
TAAAAAAAAA | AAAAAAAAAA | AAAAAAAAAC
TTAAAAAAAA | AAAAAAAAAA | AAAAAAAACC
TTTAAAAAAA | AAAAAAAAAA | AAAAAAACCC
< ----3 subs ----- > < ---- 3 subs ---- >
< -------------- 6 subs --------------- >
So, what can we say about the three groups? We can say that each one
of the members within a given group is very closely related to all of
the other members within that same group. It also seems at first
glance that the SG group is more closely related to the NSG group than
the NSG group is related to the TG group. However, it appears that
the SG group and the TG group are just as closely related as the SG
group is related to the NSG group. It appears then that the TG group
and the SG group share a common ancestor that split off about the same
time as the split occurred between the SG group and the NSG group.
Thus, although the NSG and TG groups have twice as many substitutions
as occur between the NSG and the SG groups, their common ancestor is
no more removed in history than is the common ancestor of the
seemingly more closely related SG and NSG groups. In other words,
groups that are separated by only 10 substitutions can have the same
common ancestor as a group that is separated by 20 substitutions were
10 of these substitutions are at completely different locations. If
we added other groups, we could create groups that have completely
different substitutions involving completely different locations that
still split off at about the same point in time.
It seems then that very different and widely varied DNA substitutions
may occur and yet this might mean very little as far as one's ability
to extrapolate too much as far as a time calculation from a common
ancestor. It also seems like species boundaries cannot be based on
such differences that occur in "highly variable" portions of DNA that
have little to do with actual function or phenotypic expression.
Sean
Sean Pitman M.D.
> The doctor has used overlapping ranges of human and Neandertal to
> conclude that Neandertals are human. Now, I am hearing that human
> and chimps ranges also overlapped. So, basically, if Neandertals
> are human, then humans are chimps.
Actually the overlap in range means that mtDNA sequencing cannot be
used to draw any kind of reliable species boundary. Some such
sequences are almost identical between different species, and yet some
such sequences are very much different between members of the same
species. So, it seems to me that sequence variations cannot be used
to adequately support or exclude an individual's membership within a
particular species. Neandertals cannot be proven to be human by mtDNA
sequencing nor can they be excluded as human by mtDNA sequencing.
> Don
Sean
Sean Pitman M.D.
> I think all you've shown is that the boundaries between species are often very
> fuzzy things. I also think the determination that Neanderthals are a separate
> species was made on the basis of morphology, not on genetics. Morphologically
> they're quite distinct from us; genetically they may have been (almost certainly
> were) very similar to us. In much the same way, lions and tigers are very
> closely related - we even know they can interbreed, it's been done - but they're
> undoubtedly distinct species in their own right.
I suppose that depends upon what your definition of "species" is. The
morphologic differences between Neandertals and modern humans also
seems to fall within the range of ethnic variation. Some ethnic
groups look very different from other ethnic groups. Some anatomical
features can be very much enhanced or diminished. Some interesting
and fairly distinct genetic variations also exist between certain
ethnic groups. Are these groups to be listed as different species
based on these differences?
Sean
Chris Ho-Stuart
> Adam Marczyk
>> I think all you've shown is that the boundaries between species are often very
>> fuzzy things. I also think the determination that Neanderthals are a separate
>> species was made on the basis of morphology, not on genetics. Morphologically
>> they're quite distinct from us; genetically they may have been (almost certainly
>> were) very similar to us. In much the same way, lions and tigers are very
>> closely related - we even know they can interbreed, it's been done - but they're
>> undoubtedly distinct species in their own right.
>
> I suppose that depends upon what your definition of "species" is. The
> morphologic differences between Neandertals and modern humans also
> seems to fall within the range of ethnic variation.
No, they don't. They are easily recognizable as human, but they
remain outside the range of existing ethnic variation.
> Some ethnic groups look very different from other ethnic
> groups. Some anatomical features can be very much enhanced
> or diminished. Some interesting and fairly distinct
> genetic variations also exist between certain ethnic groups.
> Are these groups to be listed as different species based on
> these differences?
No; but this is not directly relevant, because in actual fact
the morphological differences with Neanderthals are outside the
range of ethnic variation we can see today.
The question of whether or not they should be a classified as a
distinct species is to a great extent subjective. They are quite
distinct morphologically; though I do not see how you could say
they are more or less similiar genetically or morphologically.
Both by what little DNA information we can obtain, and by what
morphology is apparent, Neanderthals are plainly human, and yet
outside the range of existing humans.
Cheers -- Chris
Jon Fleming
wrote:
>On Sun, 27 Oct 2002 18:23:04 +0000 (UTC), Harlequin <use...@cox.net>
>wrote:
<snip>
>without actual numbers (hey, that's my speed), I can only give you an
>approximation of what I think it should look like. Here is how I
>would expect the isochron to look at the point where sample A moves
>into zero territory.
>
> |
> |
> | e
> | d
> | c
> | b
> a'
> |
> |
> |
> |
> |__________________________
>
>
>sample A will be a little off, yes, but as long as it has been within
>acceptable scatter along with the other samples, it should still fall
>within the acceptable scatter for the other samples.
>
>> Plot those points and see what the isochron looks
>>like. What kind of date would the isochron method give?
>
>very old date, but that is not the issue here. The issue is, will the
>identification of the isochron's intercept hold up as oldD/Di, after,
>say 500 billion years?
Yes. Unquestionably.
You are confusing the question of whether the method is correct with
the question of whether we can apply the method given the numbers we
get from our instruments.
In 500 billion years, or any number of years you care to use, if we
have exact data the Y-intercept of the isochron line will be the
oldD/Di ratio. Exactly, at solidification, now, and forever. The
method is correct.
In 500 billion years, or any number of years you care to choose, the
numbers we get from our instruments will either have small scatter and
the Y-intercept of the isochron line will be the oldD/Di ratio or an
excellent approximation thereto, or the scatter will be too large and
we will know that we cannot apply the method.
>If it doesn't, then the identification of the
>Y-intercept is incorrect.
>
>>Remember
>>the the higher the slope the higher the age. And then what if there
>>is scatter?
>
>small scatter is acceptable. And it does serve to hide the small jump
>of Sample A from its original trajectory.
>
>>If the points are scattering over the y-axis then the
>>"age" given by the method will by infinite which is nothing more than
>>saying older than what are equipment and methods can measure.
>
>why should scattering give an infinite age? Only one point jumps off
>course at the Y-intercept, but it remains within acceptable scatter,
>and the other samples continue to remain within the original
>acceptable scatter, also.
>
>>You can make up your own numbers if you like. But if you want numbers,
>>say that we are doing Rb-Sr, that Sr-87/Sr-86 is 0.7 for a through e,
>>and that the Rb-87/Sr-86 values of a through e are 0.1, 0.2, 0.3, 0.4.
>>and 0.5 respectively.
>
>no, let the above hypothetical isochron suffice for illustrating my
>point -- that the Y-intercept will change with the passage of time,
>therefore the Y-intercept cannot be oldD/Di, since oldD/Di doesn't
>change.
It illustrates what you are trying to establish, but it does not
establish your point.
Your point is a result of confusion; the question of whether the
Y-interecept of a perfect isochron is oldD/Di has nothing to do with
samples in which there is experimental error.
The question of whether we will obtain the correct oldD/Di ratio from
an analysis of real data in 500 billion years is a valid one. the
answer, demonstrated many times, is that we will obtain an excellent
approximation to the oldD/Di ratio if the scatter is small enough.
You cannot establish your point without posting a set of data in which
the scatter is acceptably small and the Y-interecept is not an
excellent approximation to oldD/Di.
<snip>
Pokemoto
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>
>wrote:
>
>snip>
>
>zoe wrote:
>
>>>consider the variation that develops instantly from intermarriages.
>>>There is no such thing as a true race, and intermarriages confirm
>>>this. I think you know this already and are just testing me, right?
>>
>>This has virtually nothing to do with the argument at hand. Why did you
>even
>>bring it up?
>
>the reason I brought it up is because you said that variation in
>extant humans is a large problem for those who think that everyone was
>created a few thousand years ago. My answer is that variation in
>sequences can occur rapidly -- just observe the morphing of races
>through intermarriage.
How many new mutations occur in everyones genome? The current estimates are
over 100. How variable were Adams chromosomes and could he have all this
variation and still be alive? A lot of the variation in the human genome do
not do very good things.
>
>From what I am reading here (hastily at that), DNA sequence variation
>is a result of single nucleotide polymorphisms, and though
>evolutionists like to consider that these variations reflect past
>mutations, I would interpret them to mean, instead, that humans have
>been programmed with the ability to vary widely in the space of a
>generation of two. I mean, there are a LOT of SNPs in evidence. A
>quote from Nature:
SNPs or whatever it doesn't matter there are a lot of them. You can't really
account for the variation except by trying to wave them away. This doesn't
work in science. What is your model and what evidence do you have to back it
up?
>
>"...comparing two human DNA sequences results in a SNP (single
>nucleotide polymorphism) every 1,000-2,000 nucleotides. That may not
>sound like much until you realize that there are 3.2 billion
>nucleotides in the human genome, which translates into 1.6 million-3.2
>million SNPs. And that's just from comparing two sequences -- the
>total number of SNPs in humans is obviously much more." Nature, Vol.
>409,15 February, 2001, p. 821
How is this variation programed in? You can't just say things like this and
expect people to listen. You have to have evidence. Where is it? It is even
worse than this for you. You don't have to compare very many humans and you
get a difference about every 300 bp, and this is just the relatively frequent
polymorphism. Get your model to account for this and tell us how the program
works.
>
>With that kind of programmed capability from the start, the human race
>can quickly go from a now-extinct Neandertal human to an extant modern
>human -- in a matter of a few thousand years.
I missed where you explained what this program was. How did this variation get
into the population when you started with just two people?
>
>>Eve had a single mitochondrial type. Demonstrate that she did not. All
>extant
>>humans are descended from Eve using your model. Where was all this
>variation
>>pre programed in?
>
>and how have you determined Eve's mitochondrial type?
She had one similar to yours and every other living human if your model is
right. What type do you think she had and what evidence do you have for this?
>
>>All Eve's daughters and sons inherited her mitochondrial mitochondrial
>type.
>>This would have been the same one as Adam's because she was essentially a
>clone
>>made from Adams rib.
>
>sounds to me like you were present, taking notes at the creation of
>the first human. How do you know exactly what was and was not
>inherited? You'd have to know exactly the richness of the genetic
>makeup of the first humans in order to form the conclusions you do.
You don't, because there is no evidence that these people even existed. But
how did Adam's and Eve's children inherit their genetic material from their
parents. Do you have any evidence that it was any different from what we
observe today. Remember what God said about it? It sounds like nothing should
have changed or God lied, or possibly some priest misrepresented what he said.
>
>>>>>>Are Neandertals human?
Snip:
>>
>>This is a totally different study on sex-linked DNA sequence of the X
>>chromosome. Do you realize that mitochondrial DNA is cytoplasmic and
>>maternally inherited.
>
>after reading a little more, I realize that now. My point still
>stands, though.
How can it still stand? You screwed up by the numbers.
>
>>Do you realize that thousands and thousands of
>>mitochondrial sequences have been and are being sequenced.
>
>last I counted in the links provided, I got a little over 2,000, not
>thousands and thousands.
Those are publication hits. How many sequences did they generate in each
paper? Remember one of the first ones had 150. They do share eachothers data,
but they also add their own data or it wouldn't be worth publishing.
>
>>It is a lot of work
>>sequencing 10,000 bp from 70 individuals, but the study is testing something
>>else, not what you think.
>>
>>What you have to ask yourself is why these different studies on different
>DNA
>>sequence tell us a consistent story about human evolution?
>
>consistent over a universe of three Neandertals? It's just not enough
>to convince me.
The point is that all the studies are consistent with our interpretation the
evolution of humans whether they are backed by 3, 70 or thousands of
sequences. What is your explanation for this?
>
>>The X chromosome is not maternally inherited. Females get one copy from
>their
>>fathers and one copy from their mothers.
>
>say that again? If the X chromosome is not maternally inherited, why
>would you say that females get one copy from their mothers?
You also get one copy from your father. If you are going to dump on genetics
you should learn something about it first. What do you think maternal
inheritance means in genetics? Look it up.
>
>>>> What type of modern human is
>>>>the most likely to fossilize today?
>>>
>>>those swept away by some flood, maybe, including our taxi-driver
>>>Neanderthal friend.
>>
>>I said most likely. What was the most likely type to be preserved in the
>flood
>>victims?
>
>there is no likely type. Floods have no preference.
This is a stupid answer and you probably know it. What was the most common
type of mitochodrial sequence that would have been preserved in the fossils of
flood victims? Explain the results that we find.
>
>>>
>>>>These aren't
>>>>just funny looking modern humans or we would find modern humans mixed in
>>>with
>>>>them.
>>>
>>>how is it possible to find modern humans mixed in with humans from a
>>>past era? Modern humans are stuck in today's setting. It would be a
>>>shock to find modern humans alongside human races from any other era.
>>>This is common sense, not science.
>>
>>That is all modern science claims, but YEC claims something different
>doesn't
>>it?
>
>I don't know what YEC claims are. I personally would not expect to
>find modern man mixed in with older human races. Modern belongs to
>modern. But that does not mean that older human races are a different
>species, just because modern man is absent. If there were giants in
>"those days" then I would expect that humans were once larger, better
>built, even more varied in genetic makeup due to environment, diet,
>lifestyle (all of which have an effect on genes), but those
>differences do not make them a different species.
Where are the giants in the fossil record?
So, Modern humans weren't burried in the flood? What separated these different
types of humans when they are often found in the same caves, but at different
layers.
>
>>So you admit that the current scientific explanation is reasonable and
>backed
>>up by the current findings, but YEC claims seem to be left out in the cold?
>
>what are YEC claims?
Everything existed at the same time a few thousand years ago.
And if you want to classify variation as
>evolution, then I could go with that. But variation has always been
>demonstrated to be within limits,
Evidence?
and the concept that a species can
>vary its way outside of its bounds and become some entirely new
>species (to wit: dinosaurs to birds, or chimps to humans) -- that is
>fantasizing, imo.
Got any evidence that it can't occur, considering all the evidence that we have
that it can? Remember DNA, remember fossils? What about homologous
structures? Why is all this evidence consistent with something that you claim
couldn't happen? What evidence do you have that is equivalent that it didn't
happen?
>>>>>>Are they some other creation?
Snip:
>>
>>No just pointing out that you have as much evidence for this assertion and
>any
>>others. It doesn't matter what you can dig up in some genetics text, but
>how
>>you are applying it. Inbreeding will not cause the genetic variation that
>is
>>observed in the Neandertals compared to modern humans. In fact it would
>seem
>>not to be inbreeding because the Neandertal sequence that we have analyzed
>are
>>about as far from each other as the most divergent modern human sequences
>are
>>from each other. These guys don't seem to be very closely related by
>>inbreeding. You might be better off suggesting that they were all selected
>>under similar environmental conditions for their genetic morphology.
>
>that is one way to look at it, but not the only way.
If you have a better explanation let us see it and the evidence to back it up.
SNip:
>>I said that they were the half gods. Reread what I wrote. They were
>supposed
>>to be the heros of old that were descended from the gods that mated with
>human
>>females.
>
>oh, okay. But that bit of info did not come from the Bible.
I guess you haven't read the Bible. It is just tossed off as something that
everyone knew about in Genesis. I don't have time to look up the passages, but
you can read the first few chapters and refresh your memory.
>>
>>It doesn't matter if they don't quailfy as "true" gods by your definition
>they
>>were called gods in the Bible.
>
>not the Nephilim and Rephaim. Do you want to quote where they were
>called gods?
I just said that they were called half gods and not gods. You are being
purposely obtuse and you know it. Your reading comprehension needs work.
>
>>Snip:
>>
Snip:
>>So what? We knew this 30 years ago using blood typing. Racial differences
>do
>>not have much of a genetic basis. This just means that we are all more
>closely
>>related to each other than some people want to believe. It says nothing
>about
>>why Neandertals fall so far outside this variation that we can't group them
>>within any of the known races.
>
>again, a couple thousand versus two or three is not a big enough
>sampling universe to come to any serious conclusions. Why do you ask
>such a tall order of me? Until there is more evidence, I see no
>reason to say that the matter is settled.
I think that you missed the point of what I said. Considering this, you can
think what ever you want, but from your track record you really don't think
very well. You should think about that for a moment.
>
>>
>>Again, this is not a mitochondrial study. You are looking at the wrong
>>experiment.
>
>right. I missed the nuclear DNA part and tied it to mtDNA. Sloppy of
>me...as usual.
>
SniP:
>>
>>As far as I know we share no MHC alleles with mice except the ones that have
>>been genetically engineered to have human MHC for tissue transplantation
>>experiments.
>
>for the most part, from what I'm reading, we, as humans, share no MHC
>alleles with each other, either. That is why rejection of grafts is
>so prevalent.
Zoe this is so stupid that you it borders on insanity. Where do children get
their alleles from. Would it be true that no humans have the same MHC alleles?
Where did you get your MHC alleles?
You may be confused by the fact that MHC is a polygenic locus and recombinants
occur, but basically children that share the same parents have 1/4 chance of
inheriting the same MHC type. This is why siblings sometime make good organ
donors for each other.
>
>> Our common ancestor with mice is so distant that we have no
>>alleles in common, but we still share alleles with chimps.
>
>not if you go by tissue rejection. The Major Histocompatibility
>Complex prevents humans from accepting transplants from chimps and
>vice versa. Maybe with abundant use of cyclosporins or other
>anti-rejection drugs, you might be able to force a fit, but it is not
>natural.
This is stupid. We aren't talking about tissue rejection we are talking about
specific alleles that are segregating. Since MHC is a polygenic locus a human
and chimp can have one locus allele the same, but have others that are very
different. The fact remains that we share this variation with chimps.
Enough to know that you are wrong and you know it. What is the source of this
contamination if they can't find a source and two different labs get the same
sequence from the same bone sample?
>
>>
>>>
>>>>Neandertal like
>>>>sequences probably do not exist in the current human population.
>>>
>>>speculation, pure speculation.
>>
>>I have more evidence for this than you have that they still exist. Like I
>said
>>I would like to see this variation in the extant population. The fact is
>that
>>from the samples that we have taken from all the diverse populations it is
>>unlikely that we will find a sequence as divergent as the Neandertal in the
>>extant population of humans.
>
>actually, it matters not one whit because, to me, it makes sense that
>humans can vary as widely as Neandertal types, Nephilim types, Rephaim
>types, modern-day types, and yet they remain humans. I'm beginning to
>think that whenever you evolutionists see a variation in species, you
>term that variation a new species. Am I correct? If so, then, yes,
>there is evolution. But the rest of your theory boils down to an
>unwarranted leap into space, with the earnest hope of jumping further
>into space by using that last leap into the air as the basis for the
>next jump.
What is the source of Nephilim mitochondrial DNA? Why is it so much different
from modern humans? You keep saying that you can explain the variation, but
you never do.
>
>snip>
>
>>You aren't talking about the same study.
>
>true. I take that back, even as I contend that it makes no difference
>in what I am saying.
It means that you are probably wrong.
>
>>Even the first Mitochondrial Eve
>>paper had sampled around 150 sequences and that was back in what, 1987? We
>>have thousands and thousands of mitochondrial D-loop sequences.
>
>thousands of D-loop sequences is not the same as sampling thousands of
>human lineages.
How do you figure? If these people did not have ancestors and relatives where
did they come from? Do you know what a lineage is? Sure they all are related
to a single sequence, but what are you trying to say about lineages. We
understand that there is only a single overall lineage that we are sampling.
The data tells us that, but we consider all the branches different sequence
lineages.
>
>snip>
>
>>Demonstrate that I am wrong. It is a possibility, no one would deny that,
>but
>>it isn't a very good possiblity or we would have found these sequences
>already.
>>
>>In more than 16 years of searching why haven't we found at least one, when
>the
>>purpose of most of the studies was to sample population variation? The
>studies
>>have sampled isolated populations from Tibet to amazon villages to Kung
>bushmen
>>in Africa. Where are the Neandertal sequences? Why are they so hard to
>find
>>if they are such a rich source of contamination?
>
>16 years of different types of studies, yes, but not 16 years of
>searching for Neandertal mtDNA in humans.
16 years seaching for any variation. All they want to find is what is out
there so we can get a better idea of population structure. We haven't found
any Neandertal sequences. What does that tell you about if they are common or
rare in the population?
Ron Okimoto
Bjoern Feuerbacher
Apparently you have abandoned the isochron threads again... Hint: you
are still wrong, and you are still unable to present even one example
(with reliable data) which would prove your assertions.
zoe_althrop wrote:
>
> On Sun, 27 Oct 2002 20:46:28 +0000 (UTC), poke...@aol.com (Pokemoto)
> wrote:
[snip]
> From what I am reading here (hastily at that), DNA sequence variation
> is a result of single nucleotide polymorphisms, and though
> evolutionists like to consider that these variations reflect past
> mutations, I would interpret them to mean, instead, that humans have
> been programmed with the ability to vary widely in the space of a
> generation of two.
There is still no evidence for such a program, and no mechanisms how
something like this could work.
[snip]
> I don't know what YEC claims are. I personally would not expect to
> find modern man mixed in with older human races.
Why not? Do you think they didn't live at the same time?
When did Neanderthals live, in your opinion? Homo erectus? Homo habilis?
> Modern belongs to
> modern. But that does not mean that older human races are a different
> species, just because modern man is absent.
How do you determine if two fossils of hominids belong to the same
species or not?
> If there were giants in
> "those days" then I would expect that humans were once larger, better
> built, even more varied in genetic makeup due to environment, diet,
> lifestyle (all of which have an effect on genes), but those
> differences do not make them a different species.
What would make them a different species?
> >So you admit that the current scientific explanation is reasonable and backed
> >up by the current findings, but YEC claims seem to be left out in the cold?
>
> what are YEC claims? And if you want to classify variation as
> evolution, then I could go with that. But variation has always been
> demonstrated to be within limits,
When did this happen, please?
> and the concept that a species can
> vary its way outside of its bounds
What are the "bounds" of a species?
> and become some entirely new
> species (to wit: dinosaurs to birds, or chimps to humans) -- that is
> fantasizing, imo.
Err, Zoe, speciation has been observed, no matter how often you deny
this.
[snip]
> >No just pointing out that you have as much evidence for this assertion and any
> >others. It doesn't matter what you can dig up in some genetics text, but how
> >you are applying it. Inbreeding will not cause the genetic variation that is
> >observed in the Neandertals compared to modern humans. In fact it would seem
> >not to be inbreeding because the Neandertal sequence that we have analyzed are
> >about as far from each other as the most divergent modern human sequences are
> >from each other. These guys don't seem to be very closely related by
> >inbreeding. You might be better off suggesting that they were all selected
> >under similar environmental conditions for their genetic morphology.
>
> that is one way to look at it, but not the only way.
What's your way?
[snip]
> >>But, at any rate, why do you consider the Nephilim to be gods? They
> >>were merely a superior race descended from giants in the earlier part
> >>of Earth's history.
> >
> >I said that they were the half gods. Reread what I wrote. They were supposed
> >to be the heros of old that were descended from the gods that mated with human
> >females.
>
> oh, okay. But that bit of info did not come from the Bible.
You don't know your Bible very well, Zoe...
Gen 6:4 "The Nephilim were on the earth in those days-and also
afterward-when the sons of God went to the daughters of men and had
children by them. They were the heroes of old, men of renown. "
[snip]
> actually, it matters not one whit because, to me, it makes sense that
> humans can vary as widely as Neandertal types, Nephilim types, Rephaim
> types, modern-day types, and yet they remain humans.
How do you determine if a life form is a human or not?
Have you ever looked at
<http://www.talkorigins.org/faqs/homs/specimen.html>?
Which of these life forms was a human, which was an ape, and where is
the insurmountable barrier?
> I'm beginning to
> think that whenever you evolutionists see a variation in species, you
> term that variation a new species.
Nonsense. Speciation is well-defined.
> Am I correct? If so, then, yes,
> there is evolution.
Err, Zoe, "evolution" simply means "a change in the allele frequency of
a population over generations".
"Speciation", "evolution" and "variation" are all different things.
> But the rest of your theory boils down to an
> unwarranted leap into space, with the earnest hope of jumping further
> into space by using that last leap into the air as the basis for the
> next jump.
Wrong.
[snip rest]
Greetings,
Bjoern
Sean Pitman M.D.
>
> [snip]
> > The third Neanderthal who's mtDNA was successfully sequenced was found
> > in a cave at Vindija, Croatia. In 2000, scientists announced the
> > mtDNA sequencing of this third Neanderthal specimen. This new
> > sequence fell within a 3.75% cluster of the first two sequences.48
> > Modern humans cluster at around 3.5%. This is a rather narrow level
> > of diversity when one compares these clusters to chimps (15%) and
> > gorillas (19%). Various human ethnic groups also have rather narrow
> > ranges of diversity in their mtDNA sequencing. Of course, the problem
> > still remains that some humans from certain of these ethic groups are
> > more closely "related" to Neanderthals than they are to certain other
> > living humans from other groups. The question remains as to who
Your mistake is that you are looking at averages. If you look at the
total ranges listed in these papers however, you will notice that the
range for human variation is larger than the smallest distance
separating the most closely related human and the Neandertal. In
other words, there are some humans living today that are separated
from each other by more substitution changes than exist between some
humans and the Neandertal. If the logic holds that a larger number of
substitutions between groups means a wider evolutionary gap, then one
should be able to argue that some humans living today are more closely
related to the Neandertal than to certain other humans living today.
Sean
Ferrous Patella
<l...@hlk.no.hj.spam.se>:
> Mark VandeWettering wrote:
>>
>> In article <3DBA4543...@hlk.no.hj.spam.se>, Sverker Johansson
>> wrote:
>> > Mark VandeWettering wrote:
>> >>
>> >> In article <3db9e545...@news-server.cfl.rr.com>, zoe_althrop
>> >> wrote:
>> >>
>> >> > is there any way to be sure that the DNA did not arise from the
>> >> > flaking off of cells from the present-day human Neanderthal?
>> >>
>> >> Chez Watt?
>> >
>> > Not really. Modern-DNA contamination is a genuine concern in
>> > paleoDNA analysis, though expressed in somewhat flaky terms here,
>> > and there have been some embarrassments in the past.
>> > But we have learnt to take rather extreme precautions:
>>
>> I'm sorry, I know I am not giving Zoe any credit for subtlety, but I
>> actually not sure that she is aware that there are no present-day
>> human Neanderthals.
>
> I'm not sure either. But there is a Swedish proverb "Even a blind hen
> occasionally finds a grain." Zoe produces quite enough unambiguous
> nonsense that we don't need to look for CW among the stuff that
> _might_ be sensible.
I think it would be more CW worthy if it was intentional.
--
Ferrous Patella
"I love the wry motto of the Paleontological Society
(meant both literally and figuratively, for hammers are the main tool
of our trade): Frango ut patefaciam - I break in order to reveal."
Stephen Jay Gould (1941-2002)
Dunno
Is there something you've read somewhere that has suggested
the Neanderthal species classificatioin is a result of
this MtDNA analysis?
Sean Pitman M.D.
> Sean Pitman M.D. <Sean...@juno.com> wrote:
> > Adam Marczyk
>
> >> I think all you've shown is that the boundaries between species are often very
> >> fuzzy things. I also think the determination that Neanderthals are a separate
> >> species was made on the basis of morphology, not on genetics. Morphologically
> >> they're quite distinct from us; genetically they may have been (almost certainly
> >> were) very similar to us. In much the same way, lions and tigers are very
> >> closely related - we even know they can interbreed, it's been done - but they're
> >> undoubtedly distinct species in their own right.
> >
> > I suppose that depends upon what your definition of "species" is. The
> > morphologic differences between Neandertals and modern humans also
> > seems to fall within the range of ethnic variation.
>
> No, they don't. They are easily recognizable as human, but they
> remain outside the range of existing ethnic variation.
Just because a particular variation does not exist today does not mean
that it is out of range of what is possible for Homo sapien gene pool.
Look at the range for dogs for example. Many kinds of dogs never
existed throughout history, until they were bred into existence in
recent times. The fact that these particular types of dogs did not
exist at a particular point in time did not mean that this particular
varieties of dog were out of range of the common gene pool for dogs.
The same is true of the human gene pool. Just because a particular
variation does not exist today, does not mean that this particular
variation is beyond the range of what is possible for the common human
gene pool to produce via genetic recombination of "static" alleles
(without relying on mutational allelic changes). The range of human
phenotypes is clearly very large just looking at the phenotypic range
that exists today. The range in height is very large, as are the
ranges in size, shape, color, etc of just about any anatomical feature
that one wishes to evaluate. For example, there have been certain
tribes of humans in recent history that have been selectively bred for
the development of extremely large posterior regions (ie: buttocks).
This selective breeding was due to the fact that slave traders that
came to this region did not take those persons with large posteriors.
Over the course of several generations, these large posteriors became
quite stunning indeed... far out of range of what any other human
population had. However, once this selective slave trading ended,
this population gradually lost its most distinctive feature and
drifted back toward the norm. Obviously then, the range of what is
possible is quite dramatic. The unique features of Neandertals may
not be so far out of range then considering that the range can be
quite impressive indeed.
> > Some ethnic groups look very different from other ethnic
> > groups. Some anatomical features can be very much enhanced
> > or diminished. Some interesting and fairly distinct
> > genetic variations also exist between certain ethnic groups.
> > Are these groups to be listed as different species based on
> > these differences?
>
> No; but this is not directly relevant, because in actual fact
> the morphological differences with Neanderthals are outside the
> range of ethnic variation we can see today.
Actually, the fact that certain of the Neandertal variations are not
seen today is not directly relevant as I discussed above. Just
because something is not here today does not mean that it is out of
range. There have been many groups of humans with distinctive
features that are no longer living today. They are "extinct", but
their features are not out of range just because these features are no
longer with us.
> The question of whether or not they should be a classified as a
> distinct species is to a great extent subjective.
Exactly. That is my whole point. This mtDNA sequencing does not make
this determination any more "objective" either. Since this process is
so subjective, why is it presented as scientific "fact"?
> They are quite
> distinct morphologically;
Certainly they are.
> though I do not see how you could say
> they are more or less similar genetically or morphologically.
I'm not saying that they are more or less similar than they obviously
are. I am just saying that they might actually be within the range of
what is possible for our common human gene pool to produce. In
otherwords, they might be just another ethnic variation or expression
of the same human gene pool of phenotypic options. The mtDNA
sequencing differences has not ruled out this possibility, and neither
have their most "unique" anatomical features.
> Both by what little DNA information we can obtain, and by what
> morphology is apparent, Neanderthals are plainly human, and yet
> outside the range of existing humans.
Again, outside of the range of existing humans does not mean that
Neandertals are outside of the range of the common human gene pool
since not every possible human phenotypic that can be made is being
expressed at any one time... much less at this time.
> Cheers -- Chris
Sean
Sean Pitman M.D.
> Your conclusions are not reasonable.
>
> The data shows that a _very_ _few_ human sequences, those that are
> farthest from the human average, are closer to a _very_ _few_
> Neanderthal sequences, those that are farthest from the Neanderthal
> average, than they are to the human average.
>
> It _does_ _not_ show that any humans have Neanderthal DNA at all, it
> just shows that a few unusual humans have DNA that is closer to _but_
> _not_ _the_ _same_ as_ a few unusual Neanderthals.
>
> It definitely shows that it is _unlikely_ that "my neighbor has
> Neanderthal mtDNA -- or maybe I do". It is unlikely that your
> neighbor or you have DNA that is even _similar_ to Neanderthal DNA.
Evidently Jon, you don't understand the point of this discussion. No
one is saying that any human has the same DNA as Neandertals do. We
are talking about the range of variations between different humans and
between certain humans and Neandertals. Yes, all humans living today
are different from Neandertals. However, there are humans living
today that are more similar to Neandertals in the absolute number of
substitutions than they are to other humans living today. Also, since
there have only been three Neandertals successfully sequenced, there
really isn't any such thing as an "unusual" Neandertal sequence.
Sean
Sean Pitman M.D.
> >>http://naturalselection.0catch.com/Files/Early%20Man.html
> Once I saw that he dishonestly included some frauds on his page, I saw
> no reason to read the rest of it. Piltdown Man and Nebraska Man are not
> part of science. If the good doctor doesn't know that, then he is
> hopelessly confused. If he knows it but implies by positioning that the
> rest of the evidence is equally suspect, then he is being utterly
> dishonest.
The theory of evolution is a historical theory as well as a modern
theory that started with historical evidence that was interpreted
historically by well educated men of "science". My purpose of
including historical frauds such as Piltdown Man, and the confusion of
Nebraska Man, are to show that brilliant minds and scientists in every
age have been hopelessly duped, sometimes by their own wishful
thinking, by "evidence" that has later proved to be very weak even
considering the limitations of the day. Scientists in every age have
been subject to biases. Sometimes these biases get even very
brilliant and well educated men into real embarrassing situations. No
one is immune from this problem of bias. Perhaps the same will be
said of modern science and scientists as those of the future look back
on us. I am saying that some of the claims of modern scientists
overreach themselves just as the claims of past scientists overreached
themselves. Sometimes, even scientists interpret more into the
data/facts at hand than can reasonable be supported by the facts.
> Of course, no honest critic of science would refer to 50 year old books
> and selected anti-science literature, but refuse to reference current
> science journal articles. I doubt that he actually read the Richmond
> paper.
Actually, since the past tends to shed light on the current and future
state of affairs, it is very reasonable to see how human nature has
acted in the past and consider if it may not be influencing current
thinking and trends as well. In looking at the past, historical
references are quite helpful. Since you didn't read past my blurb on
Nebraska Man, you wouldn't know if I referenced "current" science
journal articles or not now would you? The fact of the matter is that
this current thread discussion in this discussion group is all about
Neandertal mtDNA, which is quite current.
I do understand though why you do not like to see or have others read
about the jerky starts of evolutionary "science". Of course this does
not mean that the theory of evolution is wrong, just that even this
theory is not immune from mistakes, even significant mistakes.
Likewise, the current theories proposed should not be immune from
skepticism and/or detailed attempts to disprove the hypothesis of
those who present their ideas as "scientific." Science is mostly
about trying to disprove hypothesis. Once a person stops trying to
disprove the statements of science, these statements leave the realm
of science and turn into something almost religious or holy... much
like a religious dogma. In my opinion, religion itself should be
treated as a science. As a science, I think that one's own religion
should be constantly challenged, questioned, and revised. If one's
religion is not personally testable in some way, or aspects of it
disprovable, then, in my opinion, it is not worth very much.
Sean
Dunk
As the groups coexisted, one of the best tests of same vs different
species is whether there was any appreciable interbreeding. So far,
the genetic data indicate that there was not.
Dunk
John Harshman
True. But the logic doesn't hold. Even with a molecular clock (if there
is one, which is uncertain), there is stochastic variation. The shorter
the sequence, the greater the magnitude of the variation. By chance,
some mitochondrial lineages have experienced more mutations (or, really,
more fixations) than others. If the clock were perfect, smaller distance
would equal closer relationship. But the clock isn't perfect. So H.
sapiens lineages with lots of mutations may be farther from other H.
sapiens lineages with few mutations than the latter are to a
30,000-year-old Neanderthal lineage. No surprise, necessarily. It
depends on the time of separation and the variation in the clock.
Visual aid:
H. sapiens 1
|
|
|
|
| H. sapiens 2
|
| |
| |
| | Neanderthal
\ /
---------- |
| |
| |
\ /
-----------------
|
|
to Pan outgroup
H. sapiens 2 is "closer" to Neanderthal than to H. sapiens 1 (count the
|'s). But H. sapiens still forms a group excluding Neanderthals.
Now, there are all sorts of remaining questions here. There are
mitochondrial groups within H. sapiens (though they are only
statistically valid groups -- no human group has only distinct
haplotypes), and we don't call them separate species. Mitochondrial
distances or mitochondrial clusterings alone don't make separate
species. But they do provide one clue about species status. Neanderthals
might be a separate species even if there were shared mt haplotypes with
H. sapiens, or they might be the same species even if there weren't. But
the separation of haplotypes is one more piece of evidence for species
status.
What would be really great would be to sequence a lot more ancient DNA:
more Neanderthal specimens to establish the range of Neanderthal
haplotypes, and a lot of H. sapiens specimens of the same age and
geographic region. And especially any supposed (on morphological
grounds) hybrids. If there was gene flow, that's where to look for it.
It also gets around the problem that we expect the range of H. sapiens
variation to be narrower now than it was 30k years ago.
--
*Note the obvious spam-defeating modification
to my address if you reply by email.
John Harshman
You realize that this statement makes no sense outside a creationist
context. It implicitly assumes there are limits to genetic variation
within a "kind". But we see no sign that such limits exist.
> Look at the range for dogs for example. Many kinds of dogs never
> existed throughout history, until they were bred into existence in
> recent times. The fact that these particular types of dogs did not
> exist at a particular point in time did not mean that this particular
> varieties of dog were out of range of the common gene pool for dogs.
> The same is true of the human gene pool. Just because a particular
> variation does not exist today, does not mean that this particular
> variation is beyond the range of what is possible for the common human
> gene pool to produce via genetic recombination of "static" alleles
> (without relying on mutational allelic changes).
Whoops. Concept slippage. First, there is no recombination among
mitochondria, so there is no ability for new mitochondrial haplotypes to
be produced without mutation.
Second, much of that variation you see in dogs is known to be the result
of mutations.
Third, why are you so anxious to reject mutation as a source of
variation? Is it possible you have an agenda there?
> The range of human
> phenotypes is clearly very large just looking at the phenotypic range
> that exists today. The range in height is very large, as are the
> ranges in size, shape, color, etc of just about any anatomical feature
> that one wishes to evaluate. For example, there have been certain
> tribes of humans in recent history that have been selectively bred for
> the development of extremely large posterior regions (ie: buttocks).
> This selective breeding was due to the fact that slave traders that
> came to this region did not take those persons with large posteriors.
I doubt you can back this theory up with anything. Or can you? It sounds
really silly on its, uh, face. Why should slave traders reject big butts?
> Over the course of several generations, these large posteriors became
> quite stunning indeed... far out of range of what any other human
> population had. However, once this selective slave trading ended,
> this population gradually lost its most distinctive feature and
> drifted back toward the norm. Obviously then, the range of what is
> possible is quite dramatic. The unique features of Neandertals may
> not be so far out of range then considering that the range can be
> quite impressive indeed.
Sure. But the range is far out side anything we know today, and is
outside the range that we generally use in deciding species status in
other groups (where ecological information is absent, that is). If we
were talking about rodents, I doubt there would be a question.
> > > Some ethnic groups look very different from other ethnic
> > > groups. Some anatomical features can be very much enhanced
> > > or diminished. Some interesting and fairly distinct
> > > genetic variations also exist between certain ethnic groups.
> > > Are these groups to be listed as different species based on
> > > these differences?
> >
> > No; but this is not directly relevant, because in actual fact
> > the morphological differences with Neanderthals are outside the
> > range of ethnic variation we can see today.
>
> Actually, the fact that certain of the Neandertal variations are not
> seen today is not directly relevant as I discussed above. Just
> because something is not here today does not mean that it is out of
> range. There have been many groups of humans with distinctive
> features that are no longer living today. They are "extinct", but
> their features are not out of range just because these features are no
> longer with us.
>
> > The question of whether or not they should be a classified as a
> > distinct species is to a great extent subjective.
>
> Exactly. That is my whole point. This mtDNA sequencing does not make
> this determination any more "objective" either. Since this process is
> so subjective, why is it presented as scientific "fact"?
Where? I can think of many reasons. Science papers commonly take extreme
positions to make their results sound more interesting. Textbooks just
want conclusive answers. If anything, though, the bias has historically
been against declaring Neanderthals a separate species, because of the
theory that there could only be one hominid species living at a time.
Now we are just correcting for that bias.
> > They are quite
> > distinct morphologically;
>
> Certainly they are.
And they also lived sympatrically with modern-type humans over a fairly
broad area for a fairly long time, while keeping that distinctness. Good
argument for species status, which again wouldn't be controversial if we
were just talking about rodents.
> > though I do not see how you could say
> > they are more or less similar genetically or morphologically.
>
> I'm not saying that they are more or less similar than they obviously
> are. I am just saying that they might actually be within the range of
> what is possible for our common human gene pool to produce. In
> otherwords, they might be just another ethnic variation or expression
> of the same human gene pool of phenotypic options. The mtDNA
> sequencing differences has not ruled out this possibility, and neither
> have their most "unique" anatomical features.
This is a meaningless claim except in a creationist context. Of course
they were within the range that a human gene pool can produce, because
we all descended from a common, human ancestor. But if you're suggesting
that recombination alone can make a Neanderthal out of a modern human,
that's just not the case. We differ by a fair number of mutations, and
that's obvious at least for mitochondria.
> > Both by what little DNA information we can obtain, and by what
> > morphology is apparent, Neanderthals are plainly human, and yet
> > outside the range of existing humans.
>
> Again, outside of the range of existing humans does not mean that
> Neandertals are outside of the range of the common human gene pool
> since not every possible human phenotypic that can be made is being
> expressed at any one time... much less at this time.
Still meaningless. This argument could equally well (and poorly) be used
to claim that chimpanzees could be produced by recombination among
humans. It's an argument from ignorance. I say we have reasonable
evidence (from the billions of natural experiments currently going on)
that Neanderthals are not produced by recombination among H. sapiens
populations. We don't have to explore every point in recombination space
to determine its general shape. And that shape us, not Neanderthals or
chimps.
Floyd
> On Fri, 25 Oct 2002 17:06:41 +0000 (UTC), "Steve LaBonne"
> <labo...@lycos.com> wrote:
>
> > (neither OJ nor Jurassic Peak have
> >anything to do with the matter.)
>
> (innocent wide-eyed look) Was that the mini-series that begins with a
> dead velociraptor being found wrapped in plastic?
>
> Louann
"There was an Ichthyosaur...In the percolator!" (Would a reference to
"Sheriff Timothy Truman" be too obscure?)
-Floyd
David Jensen
Sean...@juno.com (Sean Pitman M.D.) wrote in
<fd67d42a.0210...@posting.google.com>:
>David Jensen
>
>> >>http://naturalselection.0catch.com/Files/Early%20Man.html
>
>> Once I saw that he dishonestly included some frauds on his page, I saw
>> no reason to read the rest of it. Piltdown Man and Nebraska Man are not
>> part of science. If the good doctor doesn't know that, then he is
>> hopelessly confused. If he knows it but implies by positioning that the
>> rest of the evidence is equally suspect, then he is being utterly
>> dishonest.
>
>The theory of evolution is a historical theory as well as a modern
>theory that started with historical evidence that was interpreted
>historically by well educated men of "science". My purpose of
>including historical frauds such as Piltdown Man, and the confusion of
>Nebraska Man, are to show that brilliant minds and scientists in every
>age have been hopelessly duped, sometimes by their own wishful
>thinking, by "evidence" that has later proved to be very weak even
>considering the limitations of the day.
Then if you were familiar with these examples, you would know why they
were not generally accepted and the errors were quickly corrected.
> Scientists in every age have
>been subject to biases. Sometimes these biases get even very
>brilliant and well educated men into real embarrassing situations. No
>one is immune from this problem of bias. Perhaps the same will be
>said of modern science and scientists as those of the future look back
>on us. I am saying that some of the claims of modern scientists
>overreach themselves just as the claims of past scientists overreached
>themselves. Sometimes, even scientists interpret more into the
>data/facts at hand than can reasonable be supported by the facts.
If that was your intent, that is fine, but the result of the page was to
offer false implications that all of the examples were erroneous. If you
really wanted to cover the history of hominid fossils in science, you
would have started with many older fossils and pointed out as an aside
that there were a couple of small, but quickly caught problems.
>> Of course, no honest critic of science would refer to 50 year old books
>> and selected anti-science literature, but refuse to reference current
>> science journal articles. I doubt that he actually read the Richmond
>> paper.
>
>Actually, since the past tends to shed light on the current and future
>state of affairs, it is very reasonable to see how human nature has
>acted in the past and consider if it may not be influencing current
>thinking and trends as well. In looking at the past, historical
>references are quite helpful. Since you didn't read past my blurb on
>Nebraska Man, you wouldn't know if I referenced "current" science
>journal articles or not now would you? The fact of the matter is that
>this current thread discussion in this discussion group is all about
>Neandertal mtDNA, which is quite current.
This thread is, but your page is not.
>I do understand though why you do not like to see or have others read
>about the jerky starts of evolutionary "science". Of course this does
>not mean that the theory of evolution is wrong, just that even this
>theory is not immune from mistakes, even significant mistakes.
I agree with this. I do not agree with your cherry picking and erroneous
statements about the history of science, even frauds. I get much better
information about scientific frauds from science folks than from
anti-science folks.
>Likewise, the current theories proposed should not be immune from
>skepticism and/or detailed attempts to disprove the hypothesis of
>those who present their ideas as "scientific." Science is mostly
>about trying to disprove hypothesis. Once a person stops trying to
>disprove the statements of science, these statements leave the realm
>of science and turn into something almost religious or holy... much
>like a religious dogma.
If science did not continue to test things, the frauds would not have
been caught. It is not the anti-science folks who have done anything to
discover frauds or identify better ways of learning. There is a
difference between scientific research and ignorant potshots by
religious zealots.
> In my opinion, religion itself should be
>treated as a science. As a science, I think that one's own religion
>should be constantly challenged, questioned, and revised. If one's
>religion is not personally testable in some way, or aspects of it
>disprovable, then, in my opinion, it is not worth very much.
All religions fail any kind of scientific scrutiny.
Adam Marczyk
news:fd67d42a.02102...@posting.google.com...
> Adam Marczyk
>
> > I think all you've shown is that the boundaries between species are often
very
> > fuzzy things. I also think the determination that Neanderthals are a
separate
> > species was made on the basis of morphology, not on genetics.
Morphologically
> > they're quite distinct from us; genetically they may have been (almost
certainly
> > were) very similar to us. In much the same way, lions and tigers are very
> > closely related - we even know they can interbreed, it's been done - but
they're
> > undoubtedly distinct species in their own right.
>
> I suppose that depends upon what your definition of "species" is. The
> morphologic differences between Neandertals and modern humans also
> seems to fall within the range of ethnic variation.
No, they don't. Neanderthals, for example, have heavy, bony brow ridges of a
type not seen in any currently living human.
> Some ethnic
> groups look very different from other ethnic groups.
Only in superficial features. The morphological differences between Neanderthals
and humans are not merely superficial.
> Some anatomical
> features can be very much enhanced or diminished. Some interesting
> and fairly distinct genetic variations also exist between certain
> ethnic groups.
Such as? Everything I've ever read on the subject says that genetic variation in
humans does not correlate with ethnic group.
> Are these groups to be listed as different species
> based on these differences?
--
And I want to conquer the world,
give all the idiots a brand new religion,
put an end to poverty, uncleanliness and toil,
promote equality in all of my decisions...
--Bad Religion, "I Want to Conquer the World"
http://www.ebonmusings.org ICQ: 8777843 PGP Key ID: 0x5C66F737
gen2rev
Given these examples, you can't tell.
> Lets make it more complicated:
>
> 1) AAAAAAAAAA
> 2) TTTAAAAAAA
> 3) CCCAAAAAAA
>
> Again, with three differences each. Which two belong together?
>
> 1) AAAAAAAAAAA
> 2) AAAAAAAATTT
> 3) AAACCCAAAAA
>
> Now, the differences involve different locations. Which two belong
> together?
Given these examples, you can't tell.
> Ok, according to Krings et al., humans have a range of substitution
> differences from 1 to 35. The closest distance between human and
> Neandertal sequencing is 29. It is possible therefore to find two
> humans that have more differences in their mtDNA sequences than exist
> between one (or both) of these humans and the Neandertal sequence. In
> other words, a given modern human might be 35 substitutions different
> from his neighbor, but only 29 substitutions different from our
> Neandertal friend. Am I getting it right so far?
Given the way the data has been summarized, yes, that is a possibility.
But it does not automatically mean that there *is* such a situation in
the samples used.
> Your point then is that this span of 35 differences is not as
> significant as a span of only 29 differences because of a pattern of
> differences in the 35 substitution span that is more consistent with
> one group than it is with the different pattern contained in the 29
> substitution span? In other words, you are saying that fewer
> differences can actually be interpreted, based on certain patterns, as
> a bigger difference than the absolute distance suggests?
I'm merely suggesting that the number of differences is not the only
story.
> Please, I agree that Neandertals appear to have separated from a
> common ancestor with modern humans a while back, but I do not
> understand how this can be calculated as anything farther back than
> those two modern humans who are separated by a gap that is larger.
> Perhaps you could explain this to me?
Keep in mind that not all possible subsitutions will be tolerated. Some
will be fatal, and not passed on. Also, substitutions can occasional
reverse themselves, and sometimes the same substitution will occur in
two different linages. Take this family tree:
1 2 3 4 <-Generation
agagtc----agagtt----agagat----atagat <-Lineage 1
| '-ggagtt----ggactt <-Lineage 2
| '-ggagtc <-Lineage 3
|
'-ggagtc----ggcgtc----ggcgta <-Lineage 4
It shows a change each generation. At the fourth generation, we get the
following table of differences:
Lineage
Comparison Differences
1 to 2 4
1 to 3 4
1 to 4 5
2 to 3 2
2 to 4 3
3 to 4 2
Lineage 4 was separate in the second generation, and yet there are only
two differences between it and lineage 3, whereas lineage 1 and lineage
2 which separated a generation later, have four differences.
But keep in mind that in your senario SG has not changed since the
branching event. How likely is this to have happened in reality?
> It seems then that very different and widely varied DNA substitutions
> may occur and yet this might mean very little as far as one's ability
> to extrapolate too much as far as a time calculation from a common
> ancestor. It also seems like species boundaries cannot be based on
> such differences that occur in "highly variable" portions of DNA that
> have little to do with actual function or phenotypic expression.
I suppose this depends upon your definition of "species".
> Sean
sds
"John Harshman" <harshman....@sjm.infi.net> wrote in message
news:harshman.diespamdie-...@news.infinet.mindspring.com..
Harlequin
server.cfl.rr.com:
[snip]
>>Also of interest is http://www.pnas.org/cgi/content/full/96/9/5077
>>which shows just how undiverse humans are compared to other
>>hominoids (i.e. apes). "Several chimpanzee and bonobo clades
>>(and even single social groups) have retained substantially
>>more mitochondrial variation than is seen in the entire human
>>species." This is very inconsistent with YEC dogma that
>>Pitman, AiG, ICR, and others would have us believe.
>
> I don't know, but scientists must take laypersons for fools after all.
> They make these sweeping statements on the barest whiff of data. For
> instance, they start out with: (caps mine)
>
> "In spite of the ABSENCE of relevant fossils, studies of genetic
> variation have SETTLED the question of whether humans are more closely
> related to gorillas or chimpanzees in favor of the latter (1).
> However, most such comparative studies have been based on NO MORE THAN
> SIX INDIVIDUALS of each taxon with the exception of humans."
>
> And you expect me to be impressed already with this kind of beginning?
Zoe, you are going to have to read more than a single paragraph of a
single article. Actually it does not take that many individuals to
tell the difference between humans, chimps, and gorillas. But
scientists want to know more than merely that gorillas are the outgroup
of these three taxa.
> And then you point out this statement:(caps mine)
>
> "Several chimpanzee and bonobo clades (and even single social groups)
> have retained substantially more mitochondrial variation than is seen
> in the ENTIRE human species."
>
> as if the entire human species has been checked. Come onnnn, now.
>
Zoe, get real. Scientists have sampled mtDNA from many thousands
of individual people distributed world-wide with an attempt to
sample individuals of as many ethnic groups as possible. They have
found x diversity in the mtDNA. Then they sample a few members of
a single social group of chimpanzees and find more than x diversity
in mtDNA and they find other small groups with more than x diversity.
And there are still more diversity amoung other chimpanzees.
And in the study in question they looked at 26 gorillas and 811
humans and found more mtDNA diversity in gorillas!
To put it bluntly Zoe, that is more than sufficent reason to
conclude that chimpanzees and humans have greater mtDNA
diversity than humans. The only reason to deny this is special
pleading: humans really are more diverse but by freak chance
scientist have sampled individuals that just so happen to be
alike. The probablity of is special pleading is so low as to
be safely rejected.
Your argument reminds of the bad arguments of several other
evolution deniers including one archive at:
http://www.infidels.org/library/modern/alan_hale/creationist.html
This YEC thought that Kuiper Belt was nothing more than
evolutionist dogma. And his response to an astronomer pointing
out that that three dozen of them had been discovered (at
the time of the exchange) was that three dozen objects does not
justify the existence of a belt of hundreds of millions of
objects. The astronomer's reply was simple: the telescopes
have examined only an extremely tiny portion of the possible
places to look. (And he could also pointed out that telescopes
can only spot the largest ones as well.) Thus the inference
that there really is a large belt of objects past the orbit
of Neptune is one that must be made. It is not reasonble to
suppose that telescopes just so happened to look were were some
of only a handful of objects were. You are making the
same error as that YEC did. The only way that humans could
be more diverse than chimps is that the group of people
(including European, Africans, Native American, Asians,
native Australians, and natives from Oceana, but by some
bizarre chance are fundamentally different in their mtDNA
from the rest of humanity. That is simply not reasonable.
--
Anti-spam: replace "usenet" with "harlequin2"
Harlequin
muz...@aol.com (zoe_althrop) wrote in
news:3dbcb86e....@news-server.cfl.rr.com:
>>The X chromosome is not maternally inherited. Females get one copy
>>from their fathers and one copy from their mothers.
>
> say that again? If the X chromosome is not maternally inherited, why
> would you say that females get one copy from their mothers?
--
Harlequin
news:3DBDBB93...@crosswinds.net:
[snip]
>> Lets make it more complicated:
>>
>> 1) AAAAAAAAAA
>> 2) TTTAAAAAAA
>> 3) CCCAAAAAAA
>>
>> Again, with three differences each. Which two belong together?
>>
>> 1) AAAAAAAAAAA
>> 2) AAAAAAAATTT
>> 3) AAACCCAAAAA
>>
>> Now, the differences involve different locations. Which two belong
>> together?
>
> Given these examples, you can't tell.
>
>
>> Ok, according to Krings et al., humans have a range of substitution
>> differences from 1 to 35. The closest distance between human and
>> Neandertal sequencing is 29. It is possible therefore to find two
>> humans that have more differences in their mtDNA sequences than exist
>> between one (or both) of these humans and the Neandertal sequence. In
>> other words, a given modern human might be 35 substitutions different
>> from his neighbor, but only 29 substitutions different from our
>> Neandertal friend. Am I getting it right so far?
>
> Given the way the data has been summarized, yes, that is a possibility.
> But it does not automatically mean that there *is* such a situation in
> the samples used.
[snip]
But we can rule out the situation that Pitman is suggesting from the
articles themselves. The various papers on mtDNA have done
phylogenetic analysises. If the situation was as Pitman is suggesting
is not consistent with the analysises.
Eric Rowley
> snip>
> >Zoe, it is amazing the mental gymnastics that you will go though
> >to avoid the isochron. It would take trillions of years for all
> >the parent isotope to have all decayed if we are using Rb-Sr (49
> >billion year half-life), Sm-Nd (106 billion year half-life),
> >Lu-Hf (36 billion year half-life), or Re-Os (43 billion year
> >half-life).
> this has been a hypothetical discussion, as far as I'm concerned,
> to test the definitions of the isochron. If the isochron's
> definitions cannot theoretically stand up to the test of time,
But you keep confusing theory and real world values (and your
hypothetical "Zoe world" values)
In theory (where there are no mismeasurements) the slope of the
isochron always and exactly gives the age (since solidification),
now and until the end of time.
And the y-intercept always and exactly gives the oldD/Di ratio,
now and until the end of time.
In the real world (where samples tend to have measurable P) the
slope of the isochron gives a good approximation to the age
(since solidification), now and at least a 100 billion years
into the future.
And the y-intercept gives a good approximation to the oldD/Di
ratio, now and at least a 100 billion years into the future.
As the hundreds of billions of years pass (assuming the universe
lasts that long) the approximation will get worse and worse and
the results less and less useful but that really isn't a problem
for us.
All we have to worry about is how useful the results we get _now_
are. Let future scientists worry about whether _their_ results are
useful, it doesn't affect us.
Now all your (hypothetical) scenario does is to (hypothetically)
make the approximations worse then they would otherwise be.
It DOESN'T change the meaning of the slope OR y-intercept it just
makes the values less exact.
It's up to you (if you want to cast doubts on the usefulness of the
isochron (as a measure of age since solidification)) to show that
it can make the approximations worse enough for them to become bad
approximations (without making the scatter great enough to make it
obvious that they are bad approximations).
> if its intercept will change with the sufficient passage of time,
> then the identification of the Y-intercept has to be in error,
Just the identification of the REAL WORLD Y-intercept as EXACTLY
oldD/Di, but nobody is claiming that.
> is how I see it.
> >You appear to be imagining the trajectory of a single point
> >without calculation where all the other points will be at the
> >same time.
> no, I said, "...the trajectories (plural) of the other samples
> will have their intercept correspond to the approximate intercept
> of the exhausted-P sample."
But what you're missing is that the other samples intercept will
also (almost) exactly correspond to the "correct" intercept of the
sample that never had any P.
The measured intercept (including your "exhausted-P sample") will
be somewhere inbetween your "exhausted-P sample" and the "correct"
position (and probably closer to the "correct" position) and it will
either be close enough to the "correct" position that it will be a
good approximation or the scatter will be large enough that it will
be obvious that the results are unreliable.
So, no problem!
>I am not concentrating on the
> trajectory of a single point.
> >By the time that enough time has passed to drive one of those
> >points that was not initially by the y-intercept to being on the
> >y-intercept (within measurement errors) the entire isochron will
> >have a very high slope and thus the entire isochron will be
> >close to the y-intercept. The result
> >of such a test is likely to be "infinite" age.
> not yet. Infinite would be when all samples end up in the
> unmeasurable P region and appear to be zero. The height of the
> slope is not being addressed here, but the fact that if the
> intercept APPEARS to change (due to instrumental failings) then
> it cannot therefore be identified as oldD/Di.
Nonsense!
ALL measurements are approximations, therefore all calculations
based on measurements are approximations!
The only relevant question is, does the isochron give good or bad
approximations to the real age (since solidification) and oldD/Di?
Even if you could show that your hypothetical scenario caused the
isochron to give bad approximations (which you have failed to do)
it would still only affect isochrons where at least one sample had
unmeasurably little P and wouldn't cause a problem for the majority
of cases.
> >Here is some homework for you.
> >
> >Let us imagine the following diagram.
> >
> > |
> > |
> > |
> > |
> > |
> > |
> > a'
> > |
> > | a b c d e
> > |
> > |
> > |__________________________
> >
> >
> >a, b, c, d, and e are the points at time zero.
> >
> >a' is where a will be in the far distant future (of time zero).
> >(It might be actually lower or higher up on the y-axis since
> >the exact location where a's tragectory will hit the y-axis will
> >have to be calculated.)
> >The your homework problem is to figure out where b', c', d',
> >and e' are.
> without actual numbers (hey, that's my speed), I can only give
> you an approximation of what I think it should look like. Here is
> how I would expect the isochron to look at the point where sample
> A moves into zero territory.
> |
> |
> | e
> | d
> | c
> | b
> a'
> |
> |
> |
> |
> |__________________________
You've got samples b, c, d and e lined up towards a point too
high on the y-axis.
|
|
| e
| d
| c
| b
a'
|
*
|
|
|__________________________
Would be more like it,
samples b, c, d and e would still be lined up towards the
original (correct) y-intercept (marked by a "*"), since they
aren't mismeasured there is nothing to pull them "off course".
Now the scatter in this graph is way to high and it is patently
obvious that sample a is the odd man out.
If one were to start over with sample a closer to the y-axis
then the scatter would be smaller but so would the error.
Demonstrating once again that your hypothetical problem for
isochron dating isn't a problem even in your unlikely and
unrealistic scenario.
Either the introduced error is too small to make much difference
or the scatter is so large that the unreliability of the result
is detected and the result not trusted.
> sample A will be a little off, yes, but as long as it has been
> within acceptable scatter along with the other samples, it should
> still fall within the acceptable scatter for the other samples.
Which means it will still be close to the correct oldD/Di point on
the y-axis and the error in calculated oldD/Di will be small.
> > Plot those points and see what the isochron looks like. What
> >kind of date would the isochron method give?
> very old date, but that is not the issue here. The issue is, will
> the identification of the isochron's intercept hold up as
> oldD/Di, after, say 500 billion years?
Yes, in theory the theoretical intercept will still be exactly the
value of oldD/Di and in the real world the real world intercept will
still be approximatly oldD/Di. However if we are talking Rb/Sr dating
the slope will be at least 1213 and the approximation will probably
be so bad that the values are unusable but that has no bearing on how
useful the method is _now_.
>If it doesn't, then the
> identification of the Y-intercept is incorrect.
No, it just means that, in your hypothetical (unrealistic) scenario
the calculated values of oldD/Di (which isn't used in isochron dating
anyway) aren't exactly correct, you have to show that the error can
be big enough to matter without the scatter becoming too large if you
want anyone to accept that there might be a problem.
And even if there _were_ a problem it would have a _very_ simple
solution, just don't use any samples that don't have measurable
amounts of P. Then there will be no samples with measuring errors
due to "appearant decay to zero" and all the samples will line up
towards the correct oldD/Di intercept (with a little natural scatter)
giving useful approximations to the correct age (since
solidification) and oldD/Di.
> >Remember
> >the the higher the slope the higher the age. And then what if
> >there is scatter?
> small scatter is acceptable. And it does serve to hide the small
> jump of Sample A from its original trajectory.
But a small jump only introduces a small error so the results are
still approximatly correct. And they don't change their meaning
just because they are only approximations.
> >If the points are scattering over the y-axis then the "age"
> >given by the method will by infinite which is nothing more than
> >saying older than what are equipment and methods can measure.
> why should scattering give an infinite age?
Not the scattering, having all the points on (or close to) the
Y-axis.
> Only one point jumps
> off course at the Y-intercept, but it remains within acceptable
> scatter, and the other samples continue to remain within the
> original acceptable scatter, also.
But then the "correct" intercept will also be within the accepable
scatter and we get an acceptable approximation to the correct value.
We never get an exact value anyways because the measurements are
never exact, just because you have made the approximation worse
doesn't mean that it is _bad_, you have to show _how much_ worse
it has gotten.
> >You can make up your own numbers if you like. But if you want
> >numbers, say that we are doing Rb-Sr, that Sr-87/Sr-86 is 0.7
> >for a through e, and that the Rb-87/Sr-86 values of a through e
> >are 0.1, 0.2, 0.3, 0.4. >and 0.5 respectively.
> no, let the above hypothetical isochron suffice for illustrating
> my point --that the Y-intercept will change with the passage of
> time, therefore the Y-intercept cannot be oldD/Di, since oldD/Di
> doesn't change.
The _real world_ Y-intercept is unlikely to be EXACTLY oldD/Di, true,
but nobody claimed it was!
To discredit the isochron you have to show that you can move the
Y-intercept enough to make it a _bad_ approximation of oldD/Di
(without increasing the scatter enough to make it obvious that it
is a bad approximation)
What's more, to discredit todays isochron results you have to show
that _todays_ isochrons give bad approximations, what happens 500
billion years from now is no concern of ours.
<snip DNA>
Eric
--
<My domain is rixtele>
Don1
Sean,
Was the purpose of the original paper to determine species boundaries
based on mtDNA substitutions or was it merely to estimate genetic
divergence?
It seems like the latter to me, even based on your first post in this
thread. However, additionally in that thread you paraphrased as
follows:
"Using this average difference as a basis for their conclusions,
Kahn and Gibbons wrote in the journal Science that these averages
put Neanderthal out of the statistical range of modern human
variation."
It seems like you are implying that Kahn and Gibbons do support the
notion of species boundaries derrived from mtDNA substitution counts.
First, did you mean to imply this? and second, can you provide a
quote from the article that you referenced which shows that Kahn and
Gibbons really feel this way about the data?
Thanks,
Don
Ursus: "What is more dangerous than famine, Doctor?"
Zaius: "The unknown."
("Beneath the Planet of the Apes" 1970)
Don1
> >Subject: Re: Neanderthal DNA
> >Path:
> >lobby!ngtf-m01.news.aol.com!ngpeer.news.aol.com!news.cis.ohio-state.edu!n
> ews.ems.psu.edu!newsfeed.stanford.edu!darwin.ediacara.org!there.is.no.cabal
> >Newsgroups: talk.origins
> >Date: Sun, 27 Oct 2002 16:05:38 +0000 Snip:
>
> >A criticism of overlapping ranges is a fair statistical criticism,
> >especially since somewhere there is an N=1. However, maybe the
> >doctor is confused about what the ranges mean? I know that I am.
> >Some details about these numbers are certainly left out. Could
> >someone clarify this point?
> >
> >
> >Thanks,
> >Don
>
> The gross similarities doesn't mean as much as the actual sequence. Chimps are
> expected to have accumulated just as many substitutions since the common
> ancestor as Humans. Neandertals would be expected to have accumulated just as
> many substitutions as modern humans minus around 30,000 years worth (the time
> since they went extinct and stopped evolving). We don't expect all lineages to
> evolve at the same rate, just by chance some may have more mutations than
> another. We are only looking at a few hundred base-pairs. Mitochondrial DNA
> has the added limitation in that transitions outnumber transversions by at
> least 10:1 and probably over 50:1 in the D-loop region. This just means that
> on a first approximation that there are really only two states possible at each
> position instead of four. This limits the information content of the sequence,
> and makes possible convergence by chance even more likely.
>
> In the case of Neandertals the sequences are close enough so that our estimates
> can be fairly accurate, and we have the added bonus that the three Neandertal
> sequences are about as closely related to each other as the most divergent
> human sequences are. This just means that even though the estimate for the
> common ancestor with Neandertals and modern humans is half a million years, all
> the Neandertal sequences are more closely related than that.
>
> This just means that at about the same time in the past (around 100,000 years
> ago) there was a mitochondrial Eve for Neandertals and modern humans, but they
> were very different mitochondrial sequences because around 400,000 years of
> evolution had occurred between them before those single mitochondrial types
> took over their respective populations. This just means that the Neandertal
> and modern humans mitochondrial types have a significantly different coelescent
> sequence. All extant modern humans share a common evolution of 400,000 years
> worth of mutations that are not shared with the Neandertal sequences.
>
> Just because a few modern human and Neandertal sequences have converged by
> chance after their respective coelescent sequence we can still tell that all
> modern humans have the basal modern human mitochondrial sequence and not the
> basal Neandertal sequence.
Thanks for all your information.
Can you quantify the statistical hypothesis that Neandertal sequences have
converged with a few modern human sequences versus a null hypothesis that
Neandertal sequences contributed to those few human sequences?
> This can be done until mutations obliterate the
> informative sites between Neandertals and modern humans. This wouldn't have
> happened to a significant extent for another million years or so of evolution
> along the lineage of Modern humans. The important thing to note is that even
> though it would become a problem a few million years in the future, it is not a
> problem now.
>
> Ron Okimoto
Pokemoto
>Path:
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This can be easily tested. All you have to do is compare the Neandertal
sequences individually to the modern human sequences in question. If the
modern Human sequences that supposedly are closer to Neandertal than they are
to other modern humans and are derived from the Neandertal sequence they should
have a fair number of the Neandertal specific substitutions and lack a fair
number of the modern human specific substitutions. This is obviously not the
case because these sequences fall with modern humans and not Neandertals in
phylogenetic analysis.
In a rough sense the branch lengths between the Neandertal and Modern Humans
reflect the amount of Neandertal and modern human specific substitutions (those
substitutions that occurred in the respective lineages after their separation).
All modern humans obviously share more of the lineage specific substitutions
with modern humans than they do with the Neandertal specific substitutions.
If you are talking about possible recombination between Neandertal sequence and
modern human sequence it could be detected, but there are no known instances of
mitochondrial recombination. There have been claims that recombination is
possible but none have been confirmed at this time. It appears that if it
occurs it must be relatively rare.
If recombination had occurred and caused the closeness between sequences we
would see this as a swap of a block of sequence. Say, half would be Neandertal
and half would be modern human. You would not expect Neandertal like sequence
scattered throughout the sequence. You expect large pieces to be exchanged and
not individual bases.
Ron Okimoto
John Harshman
wrote:
> "John Harshman" <harshman....@sjm.infi.net> wrote in message
> news:harshman.diespamdie-...@news.infinet.mindspring.com..
>
Computer hiccup?
Sean Pitman M.D.
> Again this is just gross similarity and we expect Neandertals to be the same
> distance minus 30,000 years from chimps as humans. It is the nesting of the
> sequences that is important. Just think about it for a few minutes. We expect
> just as much sequence evolution in Neandertals as modern humans since the
> common ancestor with chimps and humans. This is an expectation that is
> confirmed by this table. The exact nature of the sequence is the important
> data for any further analysis. Neandertals nest at 500,000 years with modern
> humans and chimps nest at 5-8 million years. You don't get this from gross
> similarity.
I don't have time to discuss the rest of your post right now, but I
will spend a few minutes with this comment.
According to what I've read, the calculation of the date of separation
of humans from Neandertals being around "500,000" years is in fact
based on the absolute average clustering difference between humans and
the three Neandertal mtDNA sequences. The clustering itself is based
on absolute numbers, not on the type or location of the cluster
differences. The formula used to calculate the date of divergence
does not analyze the type of mutations, only the absolute number of
mutations, to arrive at the divergence date. In other words, the same
formula could be theoretically used to calculate the divergence
between individual humans who have more of a substitution difference
than exists between some humans and Neandertals.
Sean
Steve Schaffner
> On Mon, 28 Oct 2002 18:59:29 +0000 (UTC), in talk.origins
> Sean...@juno.com (Sean Pitman M.D.) wrote in
> <fd67d42a.0210...@posting.google.com>:
> >The theory of evolution is a historical theory as well as a modern
> >theory that started with historical evidence that was interpreted
> >historically by well educated men of "science". My purpose of
> >including historical frauds such as Piltdown Man, and the confusion of
> >Nebraska Man, are to show that brilliant minds and scientists in every
> >age have been hopelessly duped, sometimes by their own wishful
> >thinking, by "evidence" that has later proved to be very weak even
> >considering the limitations of the day.
>
> Then if you were familiar with these examples, you would know why they
> were not generally accepted and the errors were quickly corrected.
Piltdown was not quickly corrected.
--
Steve Schaffner s...@genome.wi.mit.edu
Immediate assurance is an excellent sign of probable lack of
insight into the topic. Josiah Royce
David Jensen
Steve Schaffner <s...@darwin.wi.mit.edu> wrote in
<ydlpttt...@darwin.wi.mit.edu>:
>David Jensen <da...@dajensen-family.com> writes:
>
>> On Mon, 28 Oct 2002 18:59:29 +0000 (UTC), in talk.origins
>> Sean...@juno.com (Sean Pitman M.D.) wrote in
>> <fd67d42a.0210...@posting.google.com>:
>> >The theory of evolution is a historical theory as well as a modern
>> >theory that started with historical evidence that was interpreted
>> >historically by well educated men of "science". My purpose of
>> >including historical frauds such as Piltdown Man, and the confusion of
>> >Nebraska Man, are to show that brilliant minds and scientists in every
>> >age have been hopelessly duped, sometimes by their own wishful
>> >thinking, by "evidence" that has later proved to be very weak even
>> >considering the limitations of the day.
>>
>> Then if you were familiar with these examples, you would know why they
>> were not generally accepted and the errors were quickly corrected.
>
>Piltdown was not quickly corrected.
It wasn't generally accepted outside of the UK either.
howard hershey
> "Sean Pitman M.D." wrote:
>
>>gen2rev <gen...@crosswinds.net> wrote in message news:<3DBC0925...@crosswinds.net>...
>>
>>>"Sean Pitman M.D." wrote:
>>>
>>>>Ron Okimoto
>>>
>>>[snip]
>
>
>
>>Lets make it more complicated:
>>
>>1) AAAAAAAAAA
>>2) TTTAAAAAAA
>>3) CCCAAAAAAA
>>
>>Again, with three differences each. Which two belong together?
>>
>>1) AAAAAAAAAAA
>>2) AAAAAAAATTT
>>3) AAACCCAAAAA
>>
>>Now, the differences involve different locations. Which two belong
>>together?
>
>
> Given these examples, you can't tell.
>
to more than the single events seen in the first, since single
mutational events sometimes change more than one nucleotide.
More importantly, none of your examples are the same as the example
given by Ron where you *can* discriminate between the degrees of
parsimony of the sequences relative to their position in ancestry.
The first example is informative wrt ancestry; your examples are
simply not informative.
Specifically, for the first example:
TCACGA ATGCGT
\ /
\2 /2
ACACGT
where ACACGT is the ancestral sequence is more parsimonious (requiring
fewer mutational events to generate the other two sequences --
specifically 4) than
ACACGT ATGCGT ACACGT TCACGA
\ / \ /
\2 /4 or \2 /4
| / | /
| / | /
TCACGA ATGCGT
where one of the other sequences is ancestral which both require 6
mutational events.
Other possibilities (where none of the above sequences are the
ancestral species) are either no more or even less parsimonious in
this simple case. This is often not true. Remember, however, that we
usually are looking only at the sequences of living organisms and
typically none of them will have the 'ancestral' sequence. They all
have undergone change since divergence. The reason we can identify
one of the sequences as a possible ancestral sequence in the above
case is because the number of changes is small enough that it is
possible for there to be an unchanged sequence.
Equally parsimonious possibilities (in the above case)where all three
sequences are considered to be modern sequences different from the
ancestral would be:
ACACGT TCACGA ATGCGT
\1 /1 /1
ACACGA ACGCGT
\1 /1
ACACGT
or
ACACGT TCACGA ATGCGT
\1 /1 /1
TCACGT ACGCGT
\1 /1
TCGCGT
It is a further *observation* that the lengths of pathways (number of
sequence changes) from putative ancestors to living organisms is
roughly identical for both lineages (if you look at enough
differences). This is consistent with the idea that most of the
changes observed are selectively neutral rather than selectively
important (part of this is because one purposely looks at sequences of
genes that perform the same function in both organisms, reducing the
likelihood that selective changes are being examined).
So a better example (and more typical) would be the sequences GCACGA,
ATTCGT, and ATAGGT. The first sequence differs from the last two by 4
sites, and the last two differ from one another at 2 sites. In this
case, assuming any one of these sequences as the ancestor is less
parsimonious than assuming that ATTCGT and ATAGGT have a common
ancestor that differs in one site from ATTCGT and in one site from
ATAGGT, namely ATACGT and that this ancestor differs from GCACGA by
three sites.
GCACGA ATTCGT
\ /
\4 /2
\ |
\ |
ATAGGT
GCACGA ATAGGT
\ /
\4 /2
\ |
\ |
ATTCGT
ATAGGT ATTCGT
\ /
\4 /4
\ /
\ /
GCACGA
Above are the cases where one of the sequences is considered
ancestral.
GCACGA ATTCGT ATAGGT
\1 \1 /1
ACACGA ATACGT
\1 /1
ACACGT
Above is an example of how they could be linked through common
ancestors in a more parsimonious way than assuming that one is
ancestral (all the modern sequences are 4 changes away from each other
rather than 6 or 8). Note that in the above example ATTCGT is
considered to have a more recent common ancestor with ATAGGT than
either is expected to have with GCACGA because they are more similar.
That is, of course, the same argument used with the fossil evidence.
What is interesting is how frequently the fossil evidence and sequence
evidence agree on similarity patterns based on the assumptions of
common descent. They do so *even when* there is a discrepancy between
the amount of divergence in phenotype and the fossil record. For
example, there are frogs that are very similar in phenotype and
apparently closely related in Africa and South America which must have
become separated when these continents moved apart. There is fossil
evidence that similar frogs did exist during the time that the
continents were together. So here we have a case where there is
little change in phenotype yet long time of divergence. At the other
extreme we have humans and chimps, that are phenotypically quite
different given the amount of time at which the fossil record says
they diverged. That is, there is (relatively speaking) much
phenotypic change in little time. Sequence information, being mostly
neutral, should be a rough measure of time since divergence. That is,
the DNA from the similar modern frogs long diverged should show
significant difference. The DNA from modern chimp and human shortly
diverged should show little difference. Guess what the observations
show?
>
>>Ok, according to Krings et al., humans have a range of substitution
>>differences from 1 to 35. The closest distance between human and
>>Neandertal sequencing is 29. It is possible therefore to find two
>>humans that have more differences in their mtDNA sequences than
exist
>>between one (or both) of these humans and the Neandertal sequence.
In
>>other words, a given modern human might be 35 substitutions
different
>>from his neighbor, but only 29 substitutions different from our
>>Neandertal friend. Am I getting it right so far?
>
>
> Given the way the data has been summarized, yes, that is a possibility.
> But it does not automatically mean that there *is* such a situation in
> the samples used.
In fact, it is unlikely that the humans with extreme deviations from
some other human sequence would be more similar to the Neanderthals
with the fewest differences from the human sequence. There is
absolutely no reason to expect that *unless* you think that the humans
with these variations represents an atavistic Neanderthal sequence.
You are making a false assumption of a linear (ladder) sequence of
changes rather than a branching sequence of changes. In the branching
sequence of changes, the number of differences between the two
*extreme* ends of the branches (assuming clockwork fixation of
sequence, selective neutrality of all changes, and a very low
probability of re-ratting) is twice what you would expect from your
linear assumption. Unfortunately, in the case of mitochondria, one
cannot assume (without evidence) any of the assumptions I made and
usually must make accomodations for failure of these assumptions to be
perfectly true.
>>But,
>>by the time you get to 10 substitutions, one might be able to pick
out
>>some sort of pattern.
>>
>>Looking at substitutions alone, lets say that I find 5 humans who
are
>>separated from 5 other humans by 10 substitutions. Lets say that
all
>>10 substitutions, in both sets of humans, affect the same nucleic
>>acids in a series of 500. One of the groups must be chosen at
random
>>to be the substitution group (SG). Lets say that the substitutions
in
>>the SG group read:
>>
>>AAAAAAAAAA
>>
>>Lets also say that these same positions in the non-substitution
group
>>(NSG) read:
>>
>>TTTTTTTTTT
In reality, if you are looking only at *modern* organisms' sequences,
half of the changes would be one lineage (say the one leading to
AAAAAAAAA) and half in the other. That means that, if these sequences
are like the norm (half due to changes in one lineage and half in the
other) rather than being atypical -- which can be possible if one only
looks at a small sequence set) neither sequence would look exactly
like the ancestral sequence. The common ancestor of humans with
Neanderthal would have this *unknown* ancestral sequence and not
either of the sequences above. Unfortunately, you also have presented
an extreme that requires 100% (or more) change in a sequence. This is
completely unrelated to what happens in mitochondria. So again you
are presenting uninformative and meaningless hypothetical examples. A
more realistic argument would involve the following: Start with a
common sequence with, say, 350 sites which are selectively neutral.
Divide into 2 *independent* population lineages. Cause mutations
(*independently* in the two lineages -- but, to make it realisitic,
assume that mutation is more likely in some of the 350 sites than
others) that occassionally get fixed in and that also can lead to
lineages with accumulating differences and a certain probability of
loss of a lineage. In the human lineage, stop this process whenever
the differences between any two human sequences represents 35 changes
from each other. Examine the differences between this human and
Neanderthal sequences and the pattern that led to it. What you will
find is that *because of the limited number of neutral sites and
different rates of mutation at particular sites* you will
*independently* have some re-ratting at particular sites and some
cases where a particular Neanderthal sequence is more similar to a
particular human one *even though* it may have reached that point by a
completely different mechanism. For example, in the human lineage a
particular G may quickly become a C (because it has a high rate of
mutation) and that may get fixed into the human population by chance
and subsequently generate the occassional lineage that reverts back to
G. In the Neanderthal lineage, you may also find the occassional
lineage branch that has a C here, but most lineages retain the
original G. That means that humans have a C in most lineages (and
rare lineages that have a G because of back-mutation) and most
Neanderthals will have a G (with rare lineages having a C). But the
Neanderthals with C at this position did not acquire it from a common
ancestor with humans that had C at that position. They acquired it
independently by a process that required several events. That is why
*some* Neanderthals may appear to have somewhat fewer than the
normative number of differences between human and Neanderthal
mitochondrial sequences.
But, again, to make your case you cannot do a simple count of
differences and *assume* that the human individuals that differ by 35
changes passed through the sequences that Neanderthals have. There is
no reason at all to think that this is the case. That *assumption* is
based on some type of erroneous linear model where humans pass through
a Neanderthal stage and where the differences between modern sequences
represent a ladder-like ancestral sequence and a more modern sequence
(with Neanderthal representing steps along this ladder) rather than a
branching evolutionary model.
[more blather using uninformative sequence changes]
sds
Marc Randolph
> >[snip]
> >They compared the Neandertal sequence to
> >"994 contemporary human mitochondrial lineages, i.e. distinct
> >sequences occuring in one or more individuals, found in
> >478 Africans, 510 Europeans, 494 Asians, 167 Native Americans,
> >and 20 individuals from Australia and Oceania..."
> >
> >In short you are completely wrong that only 70 human were compared.
> >The number for the 1997 paper was, adding them up from above, 1669
> >individual people representing 994 distinct sequences.
>
> true, you are right on the numbers there, but I would still look for a
> much larger sampling universe, and certainly not so much disparity in
> numbers between the two groups. Three Neandertal lineages to 1,669
> contemporary human lineages seems terribly unbalanced to me. Not only
> that, but I notice that of 16,569 base points, only 333 were examined.
> Is this sufficient upon which to rest your whole unwieldy theory?
>
> >And even if it was just 70, your case would still be weak. Do you
> >think that by chance they picked just freek individuals to sequence?
> >The odds of that happing are almost impossibly low.
>
> no, I don't think they picked freak individuals to sequence. But I
> would think that you would need more than three Neandertal sequences
> in order to determine if there might be some that fall within the
> range of human sequences. And, vice versa, you would need way more
> than a thousand modern sequences in order to determine if any
> Neandertal sequences might still be around -- dead or dying breed that
> they might be.
>
Howdy Zoe,
How many Neanderthal sequences many would it take to convince you?
When we reach that number, (in 2, or 5 or 10 years when enough samples
have finally been discovered), will you accept they are a different
species?
Or what if we sampled EVERY human on the planet? Would you then agree
that that the Neanderthal is a unique species?
Of course, surely you would agree that we don't need to sample every
human... only the oldest person of each "family" - after all, we know
where all the children came from. But do you really need to sequence
every oldest member? My mother and her sister know they are related -
they both look just like their mother and grew up together, so you
really only need to sequence one of them. So just using my family as
an example, by sequencing 1 person you have obtained information on 15
- and I have a small family. But my family has been in one localized
area for a long long time, and in fact, has a VERY well documented
genealogy and the family has kept close touch for several generations.
Everyone knows their 3rd and 4th cousins. Is it really necessary to
sequence every one of them? Surely you can take the sequence of one
or two of them and be pretty sure that the others will have simular
results. Now you're at 1 or 2 per 100 people. Perhaps you can see
where this is leading... there really is NOT a need to obtain samples
from everyone.
Add onto my example, the fact that many many people were married for
political (or other) reasons - and were married from vastly different
locations/backgrounds. The end result is that there has been an
incredible mixing effect over the past 2-3 thousand years as the world
population has exploded - and that mixing would result in a HUGE
number of people would have Neanderthal DNA, if it existed in the
current population. That is why scientists can confidently say that
the Neanderthal is a different species.
Marc
Sean Pitman M.D.
> We don't expect equal and constant evolution in all lineages. You
> really don't understand how the analysis is done. A sequence derived from one
> ancestral sequence will look different from one derived from a different
> ancestral sequence. Long branch lengths tend to collapse the branch lengths
> and make distantly related sequences more similar than they really are, and
> this occurs in the D-loop sequence, but we can still tell that the Neandertal
> sequences are derived from a different starting point. How else do you think
> that we can tell that the humans sequences derive from one that existed 75,000
> to 150,000 years ago and the Neandertal sequences derive from one that existed
> half a million years ago?
The calculations used to estimate the "most recent common ancestors"
or MRCAs between modern humans and Neandertals where based on absolute
number averages. The average substitution difference between modern
humans, in some of the papers, is listed at about 11. Given a
substitution rate of about "0.97 x 10^-7" (that was estimated based on
an assumed split of modern humans from chimps at around "4-5 million
years"), the average substitution difference of "11" was used to
calculated that date of the modern human common ancestor to about
"163,000 years." The average difference between humans and the
Neandertal sequence is listed at about "35" or "three times" as great
as exists between humans. Note that 163,000 times 3 is equal to
489,000. Note also that this is very similar to the estimated date of
human-Neandertal divergence given in the paper to be around "465,000
years." These are estimate divergent dates based on absolute numbers,
and not on the quality or type of the substitutions involved as you
suggest.
By this logic then, one should be able to calculate the date of common
ancestor between any two individuals. If the individuals have more
substitutions separating them, then their common ancestor would be
calculated by the above method to be farther away than for two
individuals who have fewer absolute substitutions separating them. It
seems then like this method does not work so well judging from the
fact that certain modern humans have fewer substitutions when compared
with the Neandertal than they have when compared to other modern
humans.
> >> They are
> >> related to us, they fall between modern humans and chimps.
> >
> >Actually, Neanderthals do not fall between modern humans and chimps.
> >Check your references. Neanderthals actually fall farther away from
> >chimps than humans do as far as substitution differences. From the
> >"modern human" perspective, there are fewer differences, on average,
> >between us and Neanderthals than there are between us and chimps.
>
> Idiot. This is beneath even you. If the sequences fell where you say, why
> would modern humans be 500,000 years distant from the Neandertal type common
> ancestor and 5-8 million from the chimp human ancestor.
>
> By anyones measure this is between modern humans (75,000 to 150,000) and
> chimps.
Actually, only the common ancestor of modern humans and Neandertals is
thought to fall between modern humans and chimps as far as
substitution differences. This is different than what you said. You
said that Neandertals themselves "fall between modern humans and
chimps." Obviously they do not. Neandertals are as equally separated
from chimps/bonobos in their mtDNA sequencing as modern humans are.
In fact, the Neandertal "average" is in fact slightly farther away
from chimps than humans are. Even according to the papers that you
have listed, Neandertals are in no way more similar to chimps than
modern humans are. It is hypothetically suggested that the
human-Neandertal common ancestor would be more similar chimps/bonobos
than both humans and Neandertals, but this does not have to be the
case, nor is there solid evidence to indicate that is the case. It
could equally be possible that the common ancestor to modern humans
and Neandertals would have a substitution average found somewhere
between modern humans and Neandertals that would still be equidistant
from chimps/bonobos. There is no reason, except for evolutionary
assumptions for this second scenario to be wrong. In otherwords,
there is no genetic intermediate between humans and chimps that has
been found. Neandertal mtDNA certainly doesn't show such
"intermediate" substitutions.
> Ron Okimoto
Sean
Sean Pitman M.D.
> Did you actually read the paper this purported "quote" is from? (Krings
> et al. 1997. Neandertal DNA sequences and the origin of modern humans.
> Cell, 90:19–30) You've taken three different paragraphs from pages
> 24-25, 25, and 27 and strung them all together. But these quotes are all
> available on this page at Answers In Genesis:
> http://www.answersingenesis.org/docs/4218tj_v12n1.asp
Yes, I have personally read the paper by Krings et al. I first read
the page published by AIG that you reference here. That got me
thinking. So, I went and read the paper for myself. I still liked
the quotes used by AIG, so I also used them. However, I can directly
reference Krings without quoting through a secondary reference since I
have confirmed this reference for myself. There were other statements
on the AIG page that I didn't not like or agree with. I think they
have some things confused or at least make statements that are
confusing. One might get, from reading the AIG page, that humans
overlap Neandertals as far as the actual sequences of mtDNA are
concerned. Clearly this is not the case. However, the main point
made by the AIG paper seems to be very interesting and pretty
convincing... at least for me.
Sean
Sean Pitman M.D.
> But we can rule out the situation that Pitman is suggesting from the
> articles themselves. The various papers on mtDNA have done
> phylogenetic analysises. If the situation was as Pitman is suggesting
> is not consistent with the analysises.
The "phylogenetic analysis" that was done was based on the absolute
averages of the various groups involved. The analysis did not take
into account the entire ranges involved with each group in its
creation of phylogenic trees. I am talking about the ranges here.
The ranges are interesting in that certain individuals within some
groups are more similar to individuals in other groups than they are
to certain other individuals within their own group (when looking
strictly at mtDNA substitutions alone). I find that rather
interesting. It certainly messes with the notion that these
hypothesized phylogenic relationships are as clean and neat as some
scientists would like to think they are. It also messes with the
entire notion of establishing phylogenic trees to any significant
degree of confidence when these trees are based on a single trait. As
it turns out, some phylogenies, when based on a single trait, are
completely different than the phylogenic classification of the same
creatures when a different trait is used to categorize them.
Sean
Sean Pitman M.D.
> Now, there are all sorts of remaining questions here. There are
> mitochondrial groups within H. sapiens (though they are only
> statistically valid groups -- no human group has only distinct
> haplotypes), and we don't call them separate species. Mitochondrial
> distances or mitochondrial clusterings alone don't make separate
> species. But they do provide one clue about species status. Neanderthals
> might be a separate species even if there were shared mt haplotypes with
> H. sapiens, or they might be the same species even if there weren't. But
> the separation of haplotypes is one more piece of evidence for species
> status.
Actually, since the evidence, as you just said, could be explained in
other ways, to include keeping Neandertals within the same species as
Homo sapiens, then how is this "just one more piece of evidence for
species status"? It does not speak for or against species status.
The weight of evidence really doesn't swing either way here. Even
according you your own statements here, very different species may
share very similar hypervariable mtDNA clustering and very similar
individuals within the same species may be very different in their
mtDNA hypervariable clustering. So, how does this support any
particular view of speciation?
> What would be really great would be to sequence a lot more ancient DNA:
> more Neanderthal specimens to establish the range of Neanderthal
> haplotypes, and a lot of H. sapiens specimens of the same age and
> geographic region. And especially any supposed (on morphological
> grounds) hybrids. If there was gene flow, that's where to look for it.
> It also gets around the problem that we expect the range of H. sapiens
> variation to be narrower now than it was 30k years ago.
Yes, this would be great. But, until this wonderful event happens,
hypotheses about Neandertals belonging to a different species from
modern humans on the basis of mtDNA variations, are a bit overstated
at the very least.
Sean
Chris Ho-Stuart
> Chris Ho-Stuart <host...@sky.fit.qut.edu.au> wrote in message news:<3dbc...@news.qut.edu.au>...
[snip]
>> > I suppose that depends upon what your definition of "species" is. The
>> > morphologic differences between Neandertals and modern humans also
>> > seems to fall within the range of ethnic variation.
>>
>> No, they don't. They are easily recognizable as human, but they
>> remain outside the range of existing ethnic variation.
>
> Just because a particular variation does not exist today does not mean
> that it is out of range of what is possible for Homo sapien gene pool.
What you are saying here is not what you said previously. But it is
still wrong, I would think. There are some distinctive features of
Neandertal morphology which are not ever likely to reappear in the
human gene pool.
Of course, evolutionary biology does not recognize limits on
how far descendents may diverge from an ancestral population.
But it is unlikely to the point of impossible that divergence
will simply recreate the Neandertal form.
Neandertals were very similar to modern humans, but not
within the range of existing human variation.
[snip]
>> > Some ethnic groups look very different from other ethnic
>> > groups. Some anatomical features can be very much enhanced
>> > or diminished. Some interesting and fairly distinct
>> > genetic variations also exist between certain ethnic groups.
>> > Are these groups to be listed as different species based on
>> > these differences?
>>
>> No; but this is not directly relevant, because in actual fact
>> the morphological differences with Neanderthals are outside the
>> range of ethnic variation we can see today.
>
> Actually, the fact that certain of the Neandertal variations are not
> seen today is not directly relevant as I discussed above. Just
> because something is not here today does not mean that it is out of
> range. There have been many groups of humans with distinctive
> features that are no longer living today. They are "extinct", but
> their features are not out of range just because these features are no
> longer with us.
Huh? It seems that you are looking at data a bit like this.
Here is a horrible one dimensional analogy:
H H HH H HH H H HHH H N N N
|<--- human variation --->|
You consider that we could find two existing modern humans, and
an extinct Neandertal, and find that one of the modern humans is
"closer" to the Neandertal than to the other human.
I would dispute that, frankly; but even so. It is not reasonable
to describe such a circumstance as Neandertals being "within the
range of ethnic variation".
A better analogy would be multi-dimensional
H
H H N
H H
H H N
H N
H
H
>> The question of whether or not they should be a classified as a
>> distinct species is to a great extent subjective.
>
> Exactly. That is my whole point. This mtDNA sequencing does not make
> this determination any more "objective" either. Since this process is
> so subjective, why is it presented as scientific "fact"?
The presentations I have seen are all perfectly clear. The
facts are the data on mtDNA and morphology The inference,
which is generally qualified and presented as an inference,
is that Neandertals appear to be a distinct species, on the
balance of evidence.
>> They are quite
>> distinct morphologically;
>
> Certainly they are.
>
>> though I do not see how you could say
>> they are more or less similar genetically or morphologically.
>
> I'm not saying that they are more or less similar than they obviously
> are. I am just saying that they might actually be within the range of
> what is possible for our common human gene pool to produce. In
> otherwords, they might be just another ethnic variation or expression
> of the same human gene pool of phenotypic options. The mtDNA
> sequencing differences has not ruled out this possibility, and neither
> have their most "unique" anatomical features.
I agree that on the basis of morphology, Neandertals were
ambiguous. They were quite different from any existing ethnic
groups, and not significantly closer to any one existing ethnic
group than another. That is, they were not within the range of
existing ethnic variation. But on the other hand, they were
sufficiently close that we could not rule the possibility of
them being part of one human gene pool at the time.
mtDNA evidence has shed light on the matter, and indicates
that this is unlikely; the evidence strongly suggests they
the gene pools were distinct.
>> Both by what little DNA information we can obtain, and by what
>> morphology is apparent, Neanderthals are plainly human, and yet
>> outside the range of existing humans.
>
> Again, outside of the range of existing humans does not mean that
> Neandertals are outside of the range of the common human gene pool
> since not every possible human phenotypic that can be made is being
> expressed at any one time... much less at this time.
This is plainly false.
You seem to recognize that Neandertals are outside the range of
existing ethnic variation, and have fallen back on a position
that they are within the range of what might be possible in
future variation. I don't think that makes much sense.
It is just about impossible that Neandertals might reappear out
of the existing gene pool. Neandertals had some distinctive
features which are no longer present, anywhere, within humanity.
This observation is not a sufficient basis for saying that
Neandertals were, at the time, outside of a larger common
human gene pool. Perhaps, 40,000 years ago, Neandertals and
Homo sapiens sapiens did regularly interbreed, and make up a
single large gene pool.
But with genetic studies, there is now a stronger basis for
concluding that there was minimal interbreeding, if any. This
question does remain open to further evidence, but indications
at present are strong for no significant interbreeding.
Cheers -- Chris
John Harshman
Sean...@juno.com (Sean Pitman M.D.) wrote:
> John Harshman
>
> > Now, there are all sorts of remaining questions here. There are
> > mitochondrial groups within H. sapiens (though they are only
> > statistically valid groups -- no human group has only distinct
> > haplotypes), and we don't call them separate species. Mitochondrial
> > distances or mitochondrial clusterings alone don't make separate
> > species. But they do provide one clue about species status. Neanderthals
> > might be a separate species even if there were shared mt haplotypes with
> > H. sapiens, or they might be the same species even if there weren't. But
> > the separation of haplotypes is one more piece of evidence for species
> > status.
>
> Actually, since the evidence, as you just said, could be explained in
> other ways, to include keeping Neandertals within the same species as
> Homo sapiens, then how is this "just one more piece of evidence for
> species status"? It does not speak for or against species status.
No, you are wrong. The existence of separate mitochondrial clades each
composed of a population separated on other grounds (morphology or
geography, usually) is usually considered -- in non-human biology --
fairly decent evidence for species status, though this depends on your
species concept. Separation for populations living in sympatry, as H.
sapiens and H. neanderthalensis appear to have done for some time, is
good evidence under any concept. That is, separation is good evidence
against gene flow, and lack of gene flow is a good clue to species
status.
Lack of separation, contrariwise, is not particularly good evidence of
species status, because there can indeed be mitochondrial introgresion
between good species, and because inherited polymorphisms can persist
for hundreds of thousands of years even in the absence of gene flow,
though they will eventually disappear if evolution is neutral.
> The weight of evidence really doesn't swing either way here. Even
> according you your own statements here, very different species may
> share very similar hypervariable mtDNA clustering and very similar
> individuals within the same species may be very different in their
> mtDNA hypervariable clustering. So, how does this support any
> particular view of speciation?
I'm not sure how to interpret your statements above, especially what you
mean by "very different" and "share...clustering" and "particular view
of speciation". Separation of clades is reasonable evidence of species
separation, though non-separation of clades is not very good evidence
against it.
> > What would be really great would be to sequence a lot more ancient DNA:
> > more Neanderthal specimens to establish the range of Neanderthal
> > haplotypes, and a lot of H. sapiens specimens of the same age and
> > geographic region. And especially any supposed (on morphological
> > grounds) hybrids. If there was gene flow, that's where to look for it.
> > It also gets around the problem that we expect the range of H. sapiens
> > variation to be narrower now than it was 30k years ago.
>
> Yes, this would be great. But, until this wonderful event happens,
> hypotheses about Neandertals belonging to a different species from
> modern humans on the basis of mtDNA variations, are a bit overstated
> at the very least.
Disagree. The DNA evidence is not all that strong, though only because
of the small Neanderthal sample size. But combine that with the
morphological evidence and it's much stronger. Then again, there are
many hypotheses in biology with much stronger support.
Ron Okimoto
"Sean Pitman M.D." wrote:
> than exists between some humans and Neandertals.
>
> Sean
This could be one way to do it if you took the average distance between the
Neandertals and modern humans, but you have to use a pairwise average to do it.
Your odd sequences should get averaged in or the analysis would be worthless. Why
would you let a couple of sequences skew your estimate when you know that you should
get some by chance that will give you problems. You want to take an average.
Just think for a minute. The sequences that have more substitutions between two
humans than some other human has between itself and some Neandertal sequence doesn't
mean that the modern human sequence falls within the Neandertal lineage. Look at
all the phylogenies in the papers. All of them place Neandertals on a distinct
branch of their own. There is no overlap between modern human sequences and
Neandertal sequences. Even if some modern human sequence changed to a sequence that
is close to some Neandertal sequence we can still tell that it is a modern human
sequence.
All modern humans seem to be derived from a sequence that existed around 100,000
years ago. The three Neandertal sequences are about as different from each other as
modern humans are. So they could also be derived from a sequence that existed
100,000 years ago, but it is a different sequence. These two ancestral sequences
(one for all modern humans and one for all the Neandertals) would have had 400,000
years worth of independent changes to make them very different from each other.
Essentially modern humans and Neandertals mitochondrial sequences are derived for a
very different base sequence. No matter how many substitutions have occurred in
some modern human lineages we can still tell that the base sequence is modern human
and not Neandertal. This is what the phylogeny tells you. It tells you that you
are wrong about what you think simple similarity is telling you.
Ron Okimoto
Sean Pitman M.D.
> I nomininate the following for a chez watt.
>
> muz...@aol.com (zoe_althrop) wrote in
> news:3dbcb86e....@news-server.cfl.rr.com:
>
> >>The X chromosome is not maternally inherited. Females get one copy
> >>from their fathers and one copy from their mothers.
> >
> > say that again? If the X chromosome is not maternally inherited, why
> > would you say that females get one copy from their mothers?
I think that Harlequin means that the X chromosomes are not passed on
strictly by maternal inheritance like mitochondria are.
Sean
John Harshman
> Harlequin
>
> > But we can rule out the situation that Pitman is suggesting from the
> > articles themselves. The various papers on mtDNA have done
> > phylogenetic analysises. If the situation was as Pitman is suggesting
> > is not consistent with the analysises.
>
> The "phylogenetic analysis" that was done was based on the absolute
> averages of the various groups involved.
I haven't seen the paper. Is this really true? If so, it's a poor form
of analysis, which assumes its conclusion. (Use of averages assumes
monophyly of the averaged groups, so you can't use the analysis to show
species separation.) Permit me to doubt that anyone would be so silly,
though I've been surprised before. Are you sure phylogenetic analysis
didn't use individual sequences?
> The analysis did not take
> into account the entire ranges involved with each group in its
> creation of phylogenic trees. I am talking about the ranges here.
> The ranges are interesting in that certain individuals within some
> groups are more similar to individuals in other groups than they are
> to certain other individuals within their own group (when looking
> strictly at mtDNA substitutions alone). I find that rather
> interesting. It certainly messes with the notion that these
> hypothesized phylogenic relationships are as clean and neat as some
> scientists would like to think they are.
Only if you assume an absolutely perfect molecular clock. As
demonstrated in my graphic that you deleted. Even a good poisson clock
shows variance. If you use a method of analysis that doesn't assume a
clock (as most modern methods do not) there is no problem.
> It also messes with the
> entire notion of establishing phylogenic trees to any significant
> degree of confidence when these trees are based on a single trait.
No it doesn't. Unless you consider "a DNA sequence" to be a single
trait. Which is silly. It's hundreds of traits. It's a single linkage
group, but that's another question.
> As
> it turns out, some phylogenies, when based on a single trait, are
> completely different than the phylogenic classification of the same
> creatures when a different trait is used to categorize them.
As we would expect, unless homoplasy never happens. Fortunately we
seldom base phylogenies on single traits. Do you have any examples to
the contrary? (I don't say that you couldn't find *any*; I say you can't
find many. But I do wonder if you actually know of any.)