Number of shared ERVs and creationists' arguments
gecoverr
Talk.Origins webpage (http://www.talkorigins.org/faqs/comdesc/
section4.html#retroviruses) it states that there are only 7 instances.
On the other T.O. page one can read that we have thousands of them in
common with chimpanzees (http://www.talkorigins.org/indexcc/CI/
CI141.html). So which is true and how many shared ERVs do we have?
I'm asking because many creationists (e.g. Sean Pitman) are using
argument that if we share only 7 out of 30,000 ERVs, this could be
easily attributed to chance. Can anyone help me to solve this thing
out?
Ernest Major
<1e164295-87a8-4a50...@v16g2000yqn.googlegroups.com>,
gecoverr <geco...@gmail.com> writes
>How many ERVs do we share with chimps and other primates? On
>Talk.Origins webpage (http://www.talkorigins.org/faqs/comdesc/
>section4.html#retroviruses) it states that there are only 7 instances.
I think that you're misreading it, but it's not clear what it is
intended. Perhaps is 7 (then known) sequences common to humans and
chimpanzees (and not gorillas or other primates).
>On the other T.O. page one can read that we have thousands of them in
>common with chimpanzees (http://www.talkorigins.org/indexcc/CI/
>CI141.html). So which is true and how many shared ERVs do we have?
>
>I'm asking because many creationists (e.g. Sean Pitman) are using
>argument that if we share only 7 out of 30,000 ERVs, this could be
>easily attributed to chance. Can anyone help me to solve this thing
>out?
>
>http://www.detectingdesign.com/pseudogenes.html#sheer
>
--
alias Ernest Major
gecoverr
> In message
> <1e164295-87a8-4a50-98dc-2c798f372...@v16g2000yqn.googlegroups.com>,
> gecoverr <gecov...@gmail.com> writes
>
> >How many ERVs do we share with chimps and other primates? On
> >Talk.Origins webpage (http://www.talkorigins.org/faqs/comdesc/
> >section4.html#retroviruses) it states that there are only 7 instances.
>
> I think that you're misreading it, but it's not clear what it is
> intended. Perhaps is 7 (then known) sequences common to humans and
> chimpanzees (and not gorillas or other primates).
I don't think so. If this was the case, I'm sure the author would've
stressed this fact.
John Harshman
> How many ERVs do we share with chimps and other primates? On
> Talk.Origins webpage (http://www.talkorigins.org/faqs/comdesc/
> section4.html#retroviruses) it states that there are only 7 instances.
No it doesn't. It says "There are at least seven different known
instances of common retrogene insertions between chimps and humans, and
this number is sure to grow as both these organism's genomes are
sequenced." That piece predates the release of the chimpanzee genome in
2004. The seven in the 2000 paper are from a limited sample of the genome.
> On the other T.O. page one can read that we have thousands of them in
> common with chimpanzees (http://www.talkorigins.org/indexcc/CI/
> CI141.html).
The reference in that one is from 2003, after much more data were available.
> So which is true and how many shared ERVs do we have?
The latter, though I don't know of a reference that gives a definitive
count of them all. For the older insertions, there may be quite a few
ambiguous cases too, as ERVs, like any neutrally evolving sequence,
become less recognizable over time.
> I'm asking because many creationists (e.g. Sean Pitman) are using
> argument that if we share only 7 out of 30,000 ERVs, this could be
> easily attributed to chance. Can anyone help me to solve this thing
> out?
>
> http://www.detectingdesign.com/pseudogenes.html#sheer
>
Sean doesn't understand how sampling works, and he doesn't understand
the statement being made. If you look in a small piece of the genome and
find 7, it's highly unlikely that the piece you sampled just happened to
have the only 7 and that your sample is for some reason highy biased in
favor of common descent. Chance is not a reasonable explanation, unless
you're a creationist and will believe anything that lets you ignore the
evidence.
John Harshman
humans and chimps. There were, even when that article was written, more
shared by various other branches of the primate tree. If you will look
at the figure (4.4.1) right next to the text you cited, you will see 11
more insertions shared by humans, chimps, and other primates. None of
which are included in the count of 7 human-chimp insertions.
gecoverr
> gecoverr wrote:
> > How many ERVs do we share with chimps and other primates? On
> > Talk.Origins webpage (http://www.talkorigins.org/faqs/comdesc/
> > section4.html#retroviruses) it states that there are only 7 instances.
>
> No it doesn't. It says "There are at least seven different known
> instances of common retrogene insertions between chimps and humans, and
> this number is sure to grow as both these organism's genomes are
> sequenced." That piece predates the release of the chimpanzee genome in
> 2004. The seven in the 2000 paper are from a limited sample of the genome.
Ok, my mistake. I don't have an access to these papers so I didn't
know it was taken from a limited sample. And could you tell me how
long this sample was?
>
> > On the other T.O. page one can read that we have thousands of them in
> > common with chimpanzees (http://www.talkorigins.org/indexcc/CI/
> > CI141.html).
>
> The reference in that one is from 2003, after much more data were available.
>
> > So which is true and how many shared ERVs do we have?
>
> The latter, though I don't know of a reference that gives a definitive
> count of them all. For the older insertions, there may be quite a few
> ambiguous cases too, as ERVs, like any neutrally evolving sequence,
> become less recognizable over time.
>
> > I'm asking because many creationists (e.g. Sean Pitman) are using
> > argument that if we share only 7 out of 30,000 ERVs, this could be
> > easily attributed to chance. Can anyone help me to solve this thing
> > out?
>
> >http://www.detectingdesign.com/pseudogenes.html#sheer
>
> Sean doesn't understand how sampling works, and he doesn't understand
> the statement being made. If you look in a small piece of the genome and
> find 7, it's highly unlikely that the piece you sampled just happened to
> have the only 7 and that your sample is for some reason highy biased in
> favor of common descent. Chance is not a reasonable explanation, unless
> you're a creationist and will believe anything that lets you ignore the
> evidence.
Thanks a lot for clearing this up. But I think that the site "29+
Evidences..." needs an update on the subject of ERVs. "There are at
least seven different known instances of common retrogene insertions
between chimps and humans, and this number is sure to grow as both
these organism's genomes are sequenced." may sound a bit misleading,
like there were still only 7 known instances of ERV insertions common
to both species.
gecoverr
Well, I'm not sure about it. Maybe he is counting only full-length
ERVs belonging to the K family (there are only approximately 150 full-
length ERVs in our genome, rest are partially deleted fragments). And
these 11 shown in the figure 4.4.1 can be just fragments (e.g solo
LTRs).
But I can (and I probably am) wrong on this subject.
John Harshman
> On 1 Lis, 20:08, John Harshman <jharsh...@pacbell.net> wrote:
>> gecoverr wrote:
>>> How many ERVs do we share with chimps and other primates? On
>>> Talk.Origins webpage (http://www.talkorigins.org/faqs/comdesc/
>>> section4.html#retroviruses) it states that there are only 7 instances.
>> No it doesn't. It says "There are at least seven different known
>> instances of common retrogene insertions between chimps and humans, and
>> this number is sure to grow as both these organism's genomes are
>> sequenced." That piece predates the release of the chimpanzee genome in
>> 2004. The seven in the 2000 paper are from a limited sample of the genome.
>
> Ok, my mistake. I don't have an access to these papers so I didn't
> know it was taken from a limited sample. And could you tell me how
> long this sample was?
You don't need access to the papers to know this. What part of "at
least" and "sure to grow" is unclear to you?
I don't have immediate access to any of the papers either, but the
abstracts are enough to tell you the sample is limited. For example,
Lebedev et al. sampled a number (unspecified in the abstract, but almost
certainly no more than a few 10s, given the method) of candidate loci by
PCR to find insertions throughout primates, and this was for one
particular family of ERVs only. It appears that all the insertions they
found were consistent with the standard tree, by the way.
>>> On the other T.O. page one can read that we have thousands of them in
>>> common with chimpanzees (http://www.talkorigins.org/indexcc/CI/
>>> CI141.html).
>> The reference in that one is from 2003, after much more data were available.
>>
>>> So which is true and how many shared ERVs do we have?
>> The latter, though I don't know of a reference that gives a definitive
>> count of them all. For the older insertions, there may be quite a few
>> ambiguous cases too, as ERVs, like any neutrally evolving sequence,
>> become less recognizable over time.
>>
>>> I'm asking because many creationists (e.g. Sean Pitman) are using
>>> argument that if we share only 7 out of 30,000 ERVs, this could be
>>> easily attributed to chance. Can anyone help me to solve this thing
>>> out?
>>> http://www.detectingdesign.com/pseudogenes.html#sheer
>> Sean doesn't understand how sampling works, and he doesn't understand
>> the statement being made. If you look in a small piece of the genome and
>> find 7, it's highly unlikely that the piece you sampled just happened to
>> have the only 7 and that your sample is for some reason highy biased in
>> favor of common descent. Chance is not a reasonable explanation, unless
>> you're a creationist and will believe anything that lets you ignore the
>> evidence.
>
> Thanks a lot for clearing this up. But I think that the site "29+
> Evidences..." needs an update on the subject of ERVs.
Talk to Theobald.
> "There are at
> least seven different known instances of common retrogene insertions
> between chimps and humans, and this number is sure to grow as both
> these organism's genomes are sequenced." may sound a bit misleading,
> like there were still only 7 known instances of ERV insertions common
> to both species.
It's only misleading if you simultaneously notice the "7" and ignore the
parts about "sure to grow as both these organism's genomes are
sequenced". But sure, it could use an update. Mind you, all the pairwise
comparison of genomes can show you is which ERVs are not unique to the
human lineage. Chimps would be expected to share most ERV insertions
with humans. In order to find out which ERV insertions happened on the
chimp-human branch, you would have to sequence the genomes of several
other apes and monkeys. That's why it's much more practical to find
particular loci and PCR small segments containing those loci for a
number of species.
John Harshman
Why should it matter whether they're complete? If you look at just the
titles of some of the references, you will see that some of the studies
just amplified LTRs. At any rate, it's clear that this wasn't a full
count, since he told you explicitly that he expected the count to go up
when the full genomes were published. I really don't understand your
confusion here.
A little googling shows this from PLoS1:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001026
in which the authors find 18 complete ERV-K insertions common to human
and chimp but not to rhesus. Obviously that doesn't mean they all
happened in the human-chimp lineage, but it's another number for you.
I also found, in the blogosphere, a claim that there are 200,000 ERV
insertions identifiable in the human genome, of which all but 82 can be
located also in the chimp genome, and of the ERVs in the chimp genome
all but 280 are also in the human genome. It would be nice to have a
citation for this, but there is none. (Though the 82 and 280 numbers are
almost the same as found in the chimp genome release paper.) And of
course this says nothing about when the insertions happened or their
distribution in other taxa.
John S. Wilkins
Person to ask is Abbie Smith, who blogs as ERV, since that is her
research field.
--
John S. Wilkins, Philosophy, Bond University
http://evolvingthoughts.net
But al be that he was a philosophre,
Yet hadde he but litel gold in cofre
gecoverr
>
> in which the authors find 18 complete ERV-K insertions common to human
> and chimp but not to rhesus. Obviously that doesn't mean they all
> happened in the human-chimp lineage, but it's another number for you.
>
> I also found, in the blogosphere, a claim that there are 200,000 ERV
> insertions identifiable in the human genome, of which all but 82 can be
> located also in the chimp genome, and of the ERVs in the chimp genome
> all but 280 are also in the human genome. It would be nice to have a
> citation for this, but there is none. (Though the 82 and 280 numbers are
> almost the same as found in the chimp genome release paper.) And of
> course this says nothing about when the insertions happened or their
> distribution in other taxa.
I wouldn't trust these numbers, as it would mean that there were only
82 insertions in the human lineage after human-chimp split (the number
seems to be too low for 5,000,000 years of evolution). But thanks for
the paper you linked - 18 out of 32 chimp K-family retroviruses are
shared with humans. I think that's quite impressive and it completely
demolishes Sean's argument.
But it's really astonishing that even though we have both genomes
(chimp's and human's) sequenced, you can't find statistics which would
tell e.g. how many ervs or sines do we share. That kind of information
would be quite useful.
gecoverr
>
> > in which the authors find 18 complete ERV-K insertions common to human
> > and chimp but not to rhesus. Obviously that doesn't mean they all
> > happened in the human-chimp lineage, but it's another number for you.
>
> > I also found, in the blogosphere, a claim that there are 200,000 ERV
> > insertions identifiable in the human genome, of which all but 82 can be
> > located also in the chimp genome, and of the ERVs in the chimp genome
> > all but 280 are also in the human genome. It would be nice to have a
> > citation for this, but there is none. (Though the 82 and 280 numbers are
> > almost the same as found in the chimp genome release paper.) And of
> > course this says nothing about when the insertions happened or their
> > distribution in other taxa.
>
> > > But I can (and I probably am) wrong on this subject.
>
> Person to ask is Abbie Smith, who blogs as ERV, since that is her
> research field.
> --
> But al be that he was a philosophre,
> Yet hadde he but litel gold in cofre
Thanks for the tip. I'll try to ask her.
John Harshman
Let's remember that shared retroviruses is *not* an argument for
particular relationship unless we know they aren't shared with other
primates too. But it is certainly an argument for common descent even if
we don't know the distribution.
Several papers (including the chimp genome one) make the point that
there appear to have been no active ERV families during most of the
human lineage. Note that the chimp ERVs greatly outnumber the human
ones, which should be a check on the accuracy of the conclusion; if it
were just that search algorithms were bad at finding ERVs, we would
expect them to be equally bad with the chimp. Also note that some of
those 82 unique human insertions could have been deleted in the chimp,
so that's an upper bound, not a lower one.
> But it's really astonishing that even though we have both genomes
> (chimp's and human's) sequenced, you can't find statistics which would
> tell e.g. how many ervs or sines do we share. That kind of information
> would be quite useful.
I spent all of 5 minutes looking. Don't give up yet.
g...@risky-biz.com
I'm too lazy to look, but isn't the conclusive argument against Sean
that
it's not the 7 (or whatever) number we share with chimps, but that we
don't share those with any others. And then the 10 (or whatever) that
we share with the great apes, but no others. And the ??? we share with
the rest of the primates, but no others. And the ???we share with the
rest of the mammals, but no others ...
Ron O
What needs updating is the moral fortitude of scam artists like Sean
Pitman. This guy understands that he is blowing smoke, but he is
either too mentally incomptetent to draw the proper conclusions from
his own analysis or he is purposely lying. Can't rule out insanity,
but he knows the limitations of his arguments or he would have put up
the junk that he claimed to have supporting his version of reality
that he claimed was just as good as the evidence like the pseudogene
work that supports common descent. He made the claim that he had such
evidence for what he thought happened, but always ran from putting it
forward for evaluation. He hasn't changed his web name, but he knows
that the bait and switch went down and that intelligent design is just
a bogus creationist scam. Sean claimed to have the ID science to
teach even if the other ID perps wouldn't put it forward, but he ran
from that claim too. He never put up the ID science that he claimed
to have. Sean spent over half a decade posting here running from his
own claims. It isn't like he didn't know that he was running. Every
once in a while he would break and make some stupid claim like the
evidence or the ID science was on his web page, but when asked where
he would start running again.
These are claims that he requires in order to have any legitimate
argument. Shouldn't you have an alternative? Shouldn't that
alternative be supported by evidence at least as good as the evidence
you claim isn't good enough? If you claim to have ID science to teach
to school kids shouldn't you be able to produce that science and
defend it? It doesn't take much analysis to understand just how badly
off someone such as that is.
If you are in contact with Sean ask him about his common descent
claim. Ask him for his alternative alternative to common descent and
his evidence that is just as good as evidence such as the ERV data
supporting his alternative. Ask him for the intelligent design
science that he would have taught to school kids. Don't expect much
of a reply, but if you get one come back and share it with us.
Ron Okimoto
John Harshman
Yes.
g...@risky-biz.com
I assume, of course, that we don't have the genomes yet of "all the
others", especially in the larger groups, which brings to mind a
question I once asked Sean directly. The genomes we have so far form a
natural nested hierarchy, do you think that any new ones that are
sequenced will fail to fit in such a pattern?
His answer was unsatisfactory, as I remember. He said he'd already
found the anomalies, something about a platypus (natch) and convergent
evolution of snake venom between closely related species.
It strikes me as strange, even if Sean were to prove correct in the
end, that God would supply is with such profusely abundant and clear
(but evidently deceptive) evidence for Common Descent and hide
(ambiguous) evidence against it a couple of obscure places.
Greg Guarino
Walter Bushell
<5fa79c41-b692-4596...@j18g2000yqd.googlegroups.com>,
"g...@risky-biz.com" <g...@risky-biz.com> wrote:
Entirely consistent with his actions in the Bible, I'd say.
--
The Chinese pretend their goods are good and we pretend our money
is good, or is it the reverse?