Evolution for Dummies and Christians
John
1. The scientific community would not accept evolution unless it were
soundly proved. As a theory, evolution (Darwin) is on par with plate
tectonics and the Big Bang. If origins of species were not understood,
science would say so, just as it does concerning black hole
singularities, time before the Big Bang, and life on other planets.
Science is not scheming against Christians.
2. Evolution has no baring on the existence of God, because He could
easily have created a universe complex enough to allow evolution to
proceed by natural law. The presence and manifestation of God in the
universe are not nullified by evolution.
3. Almost everything is evolving according to natural law: from the
expanding universe, to the death of stars, to the changing chemistry
of the Earth's atmosphere. Is life the only thing that doesn't evolve
by natural law -- requiring the continual "tinker toying" of God?
Evolution is a simple, elegant theory, supported by the vast majority
of scientists, an extensive fossil record, genetics, geology, biology,
microevolution (laboratory and natural), and of course, common sense.
John D. Callahan
Christian theistic evolutionist
http://www.faithreason.org/
Rubystars
"John" <john...@post.com> wrote in message
news:7a0afaa.02050...@posting.google.com...
Great post!
--
-Rubystars
"Thinking to a cult member is like being stabbed in the heart with a dagger.
It's very painful because they've been told that the mind is Satan and
thinking
is the machinery of the Devil."
Quote from:
http://www.rickross.com/reference/deprogramming/deprogramming7.html
Bob Pease
I read your article on "The First Saved Man"
Although you accept Evolution, you claim that there WAS a First "Saved" man,
sometime during human prehistory.
Please answer this.
How could a Just God decide that a guy's Mother and Father, and Family were
NOT saved.?? (based on some fact of genetics that made him the first Human)
I suspect that this is a question that you're not supposed to ask,because It
is obviously Rhetorical, and maybe the concept of God interfering in any way
with the Spiritual development of Mankind leads to inherent conflicts such
this.
My personal tack ( not original) on this is that the concept of Salvation,
Justice, and God are so vague as to leave almost all questions in this area
as Meaningless.
The best answer ( or at least IMHO) is
"I dunno, But I hope that things turn out good somehow"
RJ Pease
pz
john...@post.com (John) wrote:
> It's just common sense:
>
> 1. The scientific community would not accept evolution unless it were
> soundly proved.
Ick. I hate that word. Could we say "soundly supported by the evidence",
instead?
I'd also argue that it isn't entirely true. The scientific community
will accept erroneous theories in the absence of better ones -- witness
'gemmular inheritance'.
> As a theory, evolution (Darwin) is on par with plate
> tectonics and the Big Bang. If origins of species were not understood,
> science would say so, just as it does concerning black hole
> singularities, time before the Big Bang, and life on other planets.
> Science is not scheming against Christians.
>
> 2. Evolution has no baring on the existence of God, because He could
> easily have created a universe complex enough to allow evolution to
> proceed by natural law. The presence and manifestation of God in the
> universe are not nullified by evolution.
Well...it does have some bearing on some concepts of god. When god is
used as an explanation for physical events in the real world, there is a
collision with scientific explanations, and scientific explanations are
always better than theological ones for those kinds of events. I don't
buy into Gould's NOMA blather -- the domains *do* overlap.
>
> 3. Almost everything is evolving according to natural law: from the
> expanding universe, to the death of stars, to the changing chemistry
> of the Earth's atmosphere. Is life the only thing that doesn't evolve
> by natural law -- requiring the continual "tinker toying" of God?
>
> Evolution is a simple, elegant theory, supported by the vast majority
> of scientists, an extensive fossil record, genetics, geology, biology,
> microevolution (laboratory and natural), and of course, common sense.
Yes.
--
pz
Ferrous Patella
>
>It's just common sense:
>
>1. The scientific community would not accept evolution unless it were
>soundly proved.
Argument from authority.
>As a theory, evolution (Darwin) is on par with plate
>tectonics and the Big Bang. If origins of species were not understood,
>science would say so,
Not if there jobs depended on it being right.
>just as it does concerning black hole
>singularities, time before the Big Bang, and life on other planets.
>Science is not scheming against Christians.
>
>2. Evolution has no baring on the existence of God, because He could
>easily have created a universe complex enough to allow evolution to
>proceed by natural law. The presence and manifestation of God in the
>universe are not nullified by evolution.
It is in contradiction to a literal reading of Gen1.
>
>3. Almost everything is evolving according to natural law: from the
>expanding universe, to the death of stars, to the changing chemistry
>of the Earth's atmosphere. Is life the only thing that doesn't evolve
>by natural law -- requiring the continual "tinker toying" of God?
Naturalism is a world view in contradiction to most religions and should not
be imposed upon public school students to the exclusion of other world views.
>
>Evolution is a simple, elegant theory,
It is just that, a theory.
>supported by the vast majority of scientists,
Another argument from authority.
>an extensive fossil record, genetics, geology, biology,
>microevolution (laboratory and natural),
only by an interpretation of the data blinded by a naturalist world view.
>and of course, common sense.
How common is your "common sense"? The majority of Americans believe in
Creationism.
>John D. Callahan
--
Ferrous Patella
"Four out of five dentists recommend the Theory of Evolution."
John Wilkins
John Wilkins
> In article <7a0afaa.02050...@posting.google.com>,
> john...@post.com (John) wrote:
>
> > It's just common sense:
> >
> > 1. The scientific community would not accept evolution unless it were
> > soundly proved.
>
> Ick. I hate that word. Could we say "soundly supported by the evidence",
> instead?
>
> I'd also argue that it isn't entirely true. The scientific community
> will accept erroneous theories in the absence of better ones -- witness
> 'gemmular inheritance'.
Actually, gemmular inheritance died stillborn. Only Darwin ever accepted
it, and then only for a short while.
....
--
John Wilkins
Occasionally making sense
pz
john.w...@bigpond.com (John Wilkins) wrote:
Oh, I don't know...there was that entire period from 1860-1900 where
there was a lot of guessing about how genetics worked. Everyone was
dissatisfied with the theories, but they dabbled anyway (OK, some people
like Weismann pretty much refuted the idea of somatic inheritance, but
there were also a lot of people who didn't 'get' Weismann).
I can think of one other person who liked Darwin's genetics: Haeckel.
--
pz
macaddicted
Ferrous Patella <mail1...@pop.net> wrote:
> In article <7a0afaa.02050...@posting.google.com>, John says...
[snip]
> >2. Evolution has no baring on the existence of God, because He could
> >easily have created a universe complex enough to allow evolution to
> >proceed by natural law. The presence and manifestation of God in the
> >universe are not nullified by evolution.
>
> It is in contradiction to a literal reading of Gen1.
>
Which is why as soon as I saw the post I wished that it had been titled
" Evolution for Dummies and Biblical Literalists"
[snip]
>
> How common is your "common sense"? The majority of Americans believe in
> Creationism.
>
I tend to have little faith in what people believe as defined by polls.
That recent poll showed that there are many who are confused on
scientific issues on which there is little doubt (like how long it
takes the earth to circle the sun).
--
macaddicted
"Time may be money, but your money won't buy more time"
James Taylor
Ferrous Patella
says...
>
>In article <3cd7ff03$0$14335$4c41...@reader0.ash.ops.us.uu.net>,
>Ferrous Patella <mail1...@pop.net> wrote:
>
>> In article <7a0afaa.02050...@posting.google.com>, John says...
>
>[snip]
>
>> >2. Evolution has no baring on the existence of God, because He could
>> >easily have created a universe complex enough to allow evolution to
>> >proceed by natural law. The presence and manifestation of God in the
>> >universe are not nullified by evolution.
>>
>> It is in contradiction to a literal reading of Gen1.
>>
>
>Which is why as soon as I saw the post I wished that it had been titled
>" Evolution for Dummies and Biblical Literalists"
How 'bout "Evolution for Dummies, including Biblical Literalists" just to get
the set theory right.
>[snip]
>
>
>>
>> How common is your "common sense"? The majority of Americans believe in
>> Creationism.
>>
>I tend to have little faith in what people believe as defined by polls.
>That recent poll showed that there are many who are confused on
>scientific issues on which there is little doubt (like how long it
>takes the earth to circle the sun).
>
>--
>macaddicted
>
Just so I know that you know that I knew that, I must say, "I knew that".
Knowing what the questions were to a poll is just the first step in deciding
whether one should buy the conclusion. Also, I plead guilty to a bit of
hyperbole in interpreting polls to justify my original comment.
Tom McHale
Evolution for Dummies and Christians
Group: talk.origins Date: Tue, May 7, 2002, 5:59am (EDT+4) From:
john...@post.com (John)
The preceding is a gross oversimplification not supported by
observation. Kind really does reproduce after kind. Evidence is
available everywhere and at all times. The 23 chromosome protection is
not vioalable. Support for evolution by any number of scientists does
not change the foregoing in any manner whatsoever. Argument from
authority in not viable.
The big bang is self negating from the beginning. The basic premise of
the big bang is that time and space began at the first instants of the
big bang. Where, therefore did the necessary vacuum fluctuation take
place ? There are many other fallacies with this theory. I have prepared
a time - temperature table based on big bang postulations up to the
point where life ostensively begins and evolution presumably comes into
play. I have had to make an unacceptable number of assumptions and
presumptions in order to stay within the boundaries of the theory. The
table is mathematically correct but the probability of veracity
approaches the negligible.
The universe is not expanding. The red doppler is merely reflecting
movement of various elements and systems of the steady state. Viewed
from some different parts of the universe, the doppler would undoubtedly
be in the blue spectrum.
As to our origin on this planet, based on present knowledge, I tend to
agree with the late Professor Sir Fred Hoyle in that we were implanted
from presently unknown sources and purpose. There is no life form native
to this planet that even remotely approaches our intelligence. I am not
dogmatic on this issue but it appears to be the most logical of the many
and varied postulations.
Nick Keighley
johncall wrote:
> It's just common sense:
> >1. The scientific community would not accept evolution unless it were
> soundly proved. As a theory, evolution (Darwin) is on par with plate
> tectonics and the Big Bang. If origins of species were not understood,
> science would say so, just as it does concerning black hole
> singularities, time before the Big Bang, and life on other planets.
> Science is not scheming against Christians.
> 2. Evolution has no baring on the existence of God, because He could
> easily have created a universe complex enough to allow evolution to
> proceed by natural law. The presence and manifestation of God in the
> universe are not nullified by evolution.
> 3. Almost everything is evolving according to natural law: from the
> expanding universe, to the death of stars, to the changing chemistry of
> the Earth's atmosphere. Is life the only thing that doesn't evolve by
> natural law -- requiring the continual "tinker toying" of God?
> Evolution is a simple, elegant theory, supported by the vast majority of
> scientists, an extensive fossil record, genetics, geology, biology,
> microevolution (laboratory and natural), and of course, common sense.
Tom McHale wrote:
> The preceding is a gross oversimplification not supported by
> observation.
which part of the above post is not supported by the evidence?
> [...] Kind really does reproduce after kind.
evidence?
> [...] Evidence is available everywhere and at all times.
produce some.
> The 23 chromosome protection is
> not vioalable. Support for evolution by any number of scientists does
> not change the foregoing in any manner whatsoever. Argument from
> authority in not viable.
true argument from authority is a fallacy.
> The big bang is self negating from the beginning.
the big bang is not part of evolution
<snip big bang stuff>
> The universe is not expanding. The red doppler is merely reflecting
> movement of various elements and systems of the steady state.
yes but why is it all moving away from us (bad breath?), and why is it
movinbg away from us faster the furthur away it is? Why can't we find
anything older then 15 Byr if the universe has existed forever?
> [...] Viewed
> from some different parts of the universe, the doppler would undoubtedly
> be in the blue spectrum.
"undoubtedly"?
> As to our origin on this planet, based on present knowledge, I tend to
> agree with the late Professor Sir Fred Hoyle in that we were implanted
> from presently unknown sources and purpose.
evidence?
> [...] There is no life form native
> to this planet that even remotely approaches our intelligence.
dolphins :-)
which ones are native and which ones arn't? Was Lucy an alien?
> [...] I am not
> dogmatic on this issue but it appears to be the most logical of the many
> and varied postulations.
- twin nested hierarchy
- fossil record
- human evolution
- alien motivation
- reason for faking fossil record
- are you a weak panspermian (bacteria arrived from space then evolved)?
- or strong PS (every species was planted by aliens)
- or something else?
--
Nick Keighley
Zachriel
: the big bang is that time and space began at the first instants of the
: big bang. Where, therefore did the necessary vacuum fluctuation take
: place ? There are many other fallacies with this theory.
Generally the predictive ability of a theory gives that theory credence. For
instance, Big Bang predicted the cosmic background radiation many years
before the technology was available to actually test for it. Nevertheless
the predicted radiation was finally detected, and determined to have the
predicted heat value.
Sverker Johansson
> In article <7a0afaa.02050...@posting.google.com>, John says...
> >
> >It's just common sense:
> >
> >1. The scientific community would not accept evolution unless it were
> >soundly proved.
>
> Argument from authority.
>
> >As a theory, evolution (Darwin) is on par with plate
> >tectonics and the Big Bang. If origins of species were not understood,
> >science would say so,
>
> Not if there jobs depended on it being right.
The job security of scientists is assured by current theories
_not_ being right. If everything were fully understood, no
scientists would be needed anymore, and we would be unemployed.
Furthermore, showing that an established theory is _wrong_ and
presenting a better alternative is the main road to fame and gain
as a scientist. Just confirming old theories isn't going to get
you a Nobel.
If there really were serious cracks in the foundations of evolution,
an army of scientists would be digging away at them. Look at gravity
-- there _are_ serious and well-known cracks in the foundations of
gravity (concerning its relation to quantum theory), and digging at
those crack is a major topic in theoretical physics.
OTOH inventing cracks that aren't really there is not good
for your job security.
--
Best regards, HLK, Physics
Sverker Johansson U of Jonkoping
----------------------------------------------
Definitions:
Micro-evolution: evolution for which the evidence is so
overwhelming that even the ICR can't deny it.
Macro-evolution: evolution which is only proven beyond
reasonable doubt, not beyond unreasonable doubt.
Michael Painter
"Sverker Johansson" <l...@hlk.no.hj.spam.se> wrote in message
news:3CD956AB...@hlk.no.hj.spam.se...
> Ferrous Patella wrote:
> > In article <7a0afaa.02050...@posting.google.com>, John
says...
> > >
> > >It's just common sense:
> > >
> > >1. The scientific community would not accept evolution unless it were
> > >soundly proved.
> >
> > Argument from authority.
> >
> > >As a theory, evolution (Darwin) is on par with plate
> > >tectonics and the Big Bang. If origins of species were not understood,
> > >science would say so,
> >
> > Not if there jobs depended on it being right.
>
> The job security of scientists is assured by current theories
> _not_ being right. If everything were fully understood, no
> scientists would be needed anymore, and we would be unemployed.
> Furthermore, showing that an established theory is _wrong_ and
> presenting a better alternative is the main road to fame and gain
> as a scientist. Just confirming old theories isn't going to get
> you a Nobel.
>
> If there really were serious cracks in the foundations of evolution,
> an army of scientists would be digging away at them.
supported by the "government". Emblazoned on their flag would be FFGM.
Fame, Forture and Grant Money.
Tom McHale
In our search for origins, in so far as it is known we are confronted
with two possibilities, the big bang or the steady state. The major
problem is that neither of these theories is comprehensible to human
intelligence. We cannot comprehend the origin of the beginning.
I tend toward the steady state really by default as mathematical tables
prepared by myself and others simply do not support the premise without
resorting to probable unwarranted assumptions. The reason I am not
closing the case on the big bang is that too little is known about
quantum gravity, in fact there is presently no complete viable theory.
This could but not necessarily affect the veracity of the big bang. As I
stated in an earlier post,with adjustments the big bang on a
time-temperature basis can be brought to the point of life being
produced by inherent organic chemicals and other elements and proceeding
therefrom through evolution to us. This is so improbable as to approach
the irrational concept of faith thus leaving science which of course I
have no desire of so doing.
A viable theory of quantum gravity could bring us to the long sought
unified field or at least much closer to fruition. This of course is
most encouraging.
Tom McHale
Re: Evolution for Dummies and Christians
Group: talk.origins Date: Wed, May 8, 2002, 11:35am (EDT+4) From:
lcro...@rica.net (Zachriel)
I am aware of this background radiation but the source could be local
even though emanating from all directions. I recall when the two Bell
Labs employees discovered this radiation at Murray Hill. Much stronger
evidence will be required for specific identification.
Michael Painter
"Tom McHale" <Heyd...@webtv.net> wrote in message
news:9841-3CD...@storefull-2316.public.lawson.webtv.net...
Sure it could be local and emanating from all directions.
It could also be one invisible pink unicorn with a ray gun moving about
really really fast.
It could be that Maeve *did* create the universe yesterday.
All you have to do is deny what is known about physics.
If your ideas are even vaguely close to the truth I wonder why I need 4x the
power to go about twice as far when I use a radio or why there's a need for
more than one light at a night football game.
wf...@ptd.net
wrote:
>It's just common sense:
>
>1. The scientific community would not accept evolution unless it were
>soundly proved. As a theory, evolution (Darwin) is on par with plate
>tectonics and the Big Bang. If origins of species were not understood,
>science would say so, just as it does concerning black hole
>singularities, time before the Big Bang, and life on other planets.
>Science is not scheming against Christians.
>
>2. Evolution has no baring on the existence of God, because He could
>easily have created a universe complex enough to allow evolution to
>proceed by natural law. The presence and manifestation of God in the
>universe are not nullified by evolution.
>
now THAT makes sense. i wonder why so many right wing xtians seem to
want to tell god she couldnt use evolution to create the diversity of
life. seems they're smarter than god...
---------------------
"This difference between liberalism and conservatism
must not be obscured by the fact that in the United
States it is still possible to defend individual
liberty by defending long-established institutions.
To the liberal they are valuable not mainly because
they are long established or because they are
American but because they correspond to the
ideals which he cherishes."
F. A. Hayek in "Why I am not a Conservative"
Sverker Johansson
Much stronger evidence than just the simple local observations
of Penzias & Wilson is available. Have you kept up with the
field since 1965?
For example:
If the source were local, we would not expect to see any effects of this
background radiation at cosmological distances. If the source were indeed
Big Bang, we would expect objects at all distances to be immersed in a
radiation bath, with a specific relation between the temperature of the
radiation bath, and the redshift of the object. The Big Bang thus predicts
that objects at all distances show the effect of the background radiation
(notably certain molecular transitions being excited).
When intergalactic gas is observed, the predicted effects are seen,
and follow the expected redshift-temperature relation
(references available on request).
Nick Keighley
> In our search for origins, in so far as it is known we are confronted
> with two possibilities, the big bang or the steady state. The major
> problem is that neither of these theories is comprehensible to human
> intelligence. We cannot comprehend the origin of the beginning.
why not?
> I tend toward the steady state really by default as mathematical tables
> prepared by myself and others simply do not support the premise without
> resorting to probable unwarranted assumptions.
Steady State has no ready explanation for cosmological redshift or the
cosmic back-ground radiation. Why cannot we see any objects that are
older than
15Byr? Nor furthur than 15Bly?
I notice you tend not to respond to questions like this. Why didn't
you
respond to any of the points raised in my last post. For instance
could you
explain your theory of panspermia in more detail. Was it bacteria or
kinds or species that were implanted? And by what means (chance,
aliens? gods?), if
by a concious agency, why?
> [...] The reason I am not
> closing the case on the big bang is that too little is known about
> quantum gravity, in fact there is presently no complete viable theory.
true, but there is evidence that needs explaining
> This could but not necessarily affect the veracity of the big bang. As I
> stated in an earlier post,with adjustments the big bang on a
> time-temperature basis can be brought to the point of life being
> produced by inherent organic chemicals and other elements and proceeding
> therefrom through evolution to us. This is so improbable as to approach
> the irrational concept of faith thus leaving science which of course I
> have no desire of so doing.
I would probably disagree with this if I understood it.
> A viable theory of quantum gravity could bring us to the long sought
> unified field or at least much closer to fruition. This of course is
> most encouraging.
--
Nick Keighley
Wayne Bagguley
> In article <7a0afaa.02050...@posting.google.com>, John says...
> >
> >It's just common sense:
> >
> >1. The scientific community would not accept evolution unless it were
> >soundly proved.
>
> Argument from authority.
It's not an argument from authority, it's a statement of fact.
An argument from authority is when you say that something is
true because someone in authority says so. The poster was not
saying that the theory of evolution is right, just pointing out
that the scientific community would not accept it unless it was
backed up by sound data.
> >As a theory, evolution (Darwin) is on par with plate
> >tectonics and the Big Bang. If origins of species were not understood,
> >science would say so,
>
> Not if there jobs depended on it being right.
Scientist's jobs do depend on the theory of evolution being accurate,
there are many jobs that use the theory of evolution each and every
day.
> >just as it does concerning black hole
> >singularities, time before the Big Bang, and life on other planets.
> >Science is not scheming against Christians.
> >
> >2. Evolution has no baring on the existence of God, because He could
> >easily have created a universe complex enough to allow evolution to
> >proceed by natural law. The presence and manifestation of God in the
> >universe are not nullified by evolution.
>
> It is in contradiction to a literal reading of Gen1.
And a literanl reading of Gen1 is in contradiction with a literal
reading of Gen2 and is in contradiction with the observed world.
> >
> >3. Almost everything is evolving according to natural law: from the
> >expanding universe, to the death of stars, to the changing chemistry
> >of the Earth's atmosphere. Is life the only thing that doesn't evolve
> >by natural law -- requiring the continual "tinker toying" of God?
>
>
> Naturalism is a world view in contradiction to most religions and should not
> be imposed upon public school students to the exclusion of other world views.
Be careful to distinguish between methodological naturalism and philosophical
naturalism. Which are you opposed to and why? If you want other world views
to be included then would you object to every single religion that has ever
been invented being taught?
> >
> >Evolution is a simple, elegant theory,
>
> It is just that, a theory.
Not the "it's just a theory" claim again. Evolution is a scientific theory.
You'll do well to understand what that is some day. Evolution is also a fact.
Make sure you learn about that too.
> >supported by the vast majority of scientists,
>
> Another argument from authority.
No, just another statement of fact. You need to brush up on your fallacious
argument definitions.
> >an extensive fossil record, genetics, geology, biology,
> >microevolution (laboratory and natural),
>
> only by an interpretation of the data blinded by a naturalist world view.
A remarkably consistent and coherent interpretation of the data that stands
up to many tests and predictions that have been made. Contrast this with
creationism which lacks a clear definition. Also consider that many christians
(bang goes the naturalistic world view) accept evolution.
> >and of course, common sense.
>
> How common is your "common sense"?
> The majority of Americans believe in Creationism.
Argument from authority. Now who is using fallacious arguments?
Actually, the majority (53%) of Americans accept evolution :
http://www.cnn.com/2002/TECH/science/04/30/science.understanding.ap/index.html
This in itself does not render the theory of evolution correct, remember,
I am just pointing out that your statement is wrong.
Have a nice day.
-
Wayne
Wayne Bagguley
> The preceding is a gross oversimplification not supported by
> observation. Kind really does reproduce after kind.
Define 'kind' and the test that can be performed to distinguish
between them.
Describe the mechanism preventing one kind from evolving into
another over many generations.
> Evidence is
> available everywhere and at all times. The 23 chromosome protection is
> not vioalable.
What?
> The big bang is self negating from the beginning. The basic premise of
> the big bang is that time and space began at the first instants of the
> big bang.
The idea of the BB is that it created time and space. It is not self
negating.
> Where, therefore did the necessary vacuum fluctuation take
> place ?
Somewhere not connected with this space-time. A different one perhaps.
>There are many other fallacies with this theory. I have prepared
> a time - temperature table based on big bang postulations up to the
> point where life ostensively begins and evolution presumably comes into
> play. I have had to make an unacceptable number of assumptions and
> presumptions in order to stay within the boundaries of the theory. The
> table is mathematically correct but the probability of veracity
> approaches the negligible.
I bet it's utter BS since you've not referenced it here and since you've
not submitted it to a scientific journal. What is your PHd in again?
> The universe is not expanding.
The universe is most definitely expanding at an ever increasing rate.
> The red doppler is merely reflecting
> movement of various elements and systems of the steady state.
This contradicts the data which suggest that some things are moving
away from us faster than the speed of light.
> Viewed
> from some different parts of the universe, the doppler would undoubtedly
> be in the blue spectrum.
We do see a blue shift in some of the objects that are moving toward us
but the point is there is a relationship between the speed at which
galaxies are receding from us and their distance from us. This does not
fit with your 'static universe' hypothesis.
> As to our origin on this planet, based on present knowledge, I tend to
> agree with the late Professor Sir Fred Hoyle in that we were implanted
> from presently unknown sources and purpose. There is no life form native
> to this planet that even remotely approaches our intelligence.
I hear that dolphins are quite intelligent and have bigger brains than us.
How can you tell that they are not as 'intelligent' as us? How do you define
intelligence? Hint: people are continually arguing over what intelligence
is and can't agree on a definition or how to accurately measure it.
> I am not dogmatic on this issue
Irony overload.
> but it appears to be the most logical of
> the many and varied postulations.
It's nothing of the sort. It's an argument that lacks any substance.
-
Wayne
Wayne Bagguley
> I am aware of this background radiation but the source could be local
> even though emanating from all directions. I recall when the two Bell
> Labs employees discovered this radiation at Murray Hill. Much stronger
> evidence will be required for specific identification.
And what is its source? I don't want your random assertions which you
make up in a vain attempt to rationalise you innane hypothesis. I want
evidence, logic and reason.
Somehow I don't think I'm going to get any of those from you.
-
Wayne
Ferrous Patella
says...
Hi Wanye.
Just so you know, I was being a bit of a devil's advocate with this post. I
thought the OP was a bit condisending and indeed had used some falicies.
>mail1...@pop.net (Ferrous Patella) wrote in message
news:<3cd7ff03$0$14335$4c41069e@read
>er0.ash.ops.us.uu.net>...
>> In article <7a0afaa.02050...@posting.google.com>, John says...
>> >
>> >It's just common sense:
>> >
>> >1. The scientific community would not accept evolution unless it were
>> >soundly proved.
>>
>> Argument from authority.
>
>It's not an argument from authority, it's a statement of fact.
>An argument from authority is when you say that something is
>true because someone in authority says so. The poster was not
>saying that the theory of evolution is right, just pointing out
>that the scientific community would not accept it unless it was
>backed up by sound data.
It is still an argument from authority. It is supporting ToE by who believes
it. There are scientists who buy creationism. Mostly ones outside their field
but they are scientists who know how to use data. I do not like the "We are
scientists. Trust us." argument, mostly because most people do not understand
what it takes for a idea to be accepted the the scientific community at large.
(It was the this first point that inspired me to go into devil's advocate
mode.The rest of my responses were all "shot from the hip" stock creationist
replies, just to show that the "common sense" is not as universal as the OP
implied.
[...]
>>
>> How common is your "common sense"?
>> The majority of Americans believe in Creationism.
>
>Argument from authority. Now who is using fallacious arguments?
>
>Actually, the majority (53%) of Americans accept evolution :
>
>http://www.cnn.com/2002/TECH/science/04/30/science.understanding.ap/index.htm
l
>
>This in itself does not render the theory of evolution correct, remember,
>I am just pointing out that your statement is wrong.
I have admitted to my statement being hyperbole elsewhere. I included
theological evolutionists and OECs to make up my "majority", which of course
is not mutially excusive from the 53% in the poll you sited.
>
>Have a nice day.
So far, so good.
>Wayne
Tom McHale
Re: Evolution for Dummies and Christians
snow...@snowbird.freeserve.co.uk (Wayne Bagguley)
Heyd...@webtv.net (Tom McHale) wrote in message
news:<9841-3CD...@storefull-2316.public.lawson.webtv.net>..
I am aware of this background radiation but the source could be local
even though emanating from all directions. I recall when the two Bell
Labs employees discovered this radiation at Murray Hill. Much stronger
evidence will be required for specific identification.
>And what is its source? I don't want your random assertions which you
make up in a vain attempt to rationalise you innane hypothesis. I want
evidence, logic and reason.
Somehow I don't think I'm going to get any of those from you.<
-
Wayne <
Extraordinary claims require extraordinary evidence. Admittedly as yet I
have no specific explanation for this background radiation except that
it may be local, a possible combination of sources.
The big bang must be viewed in it's entirety relative to any specific
aspect. Credulity is stretched well beyond the limits of reason by the
big bang. It requires more faith as does evolution than any religion
organized or not and of course we are all aware that faith is an
irrational concept. Let us be rational.
Keith[bugeye]
>
> Re: Evolution for Dummies and Christians
>
> Group: talk.origins Date: Mon, May 13, 2002, 4:23pm (EDT+4) From:
> snow...@snowbird.freeserve.co.uk (Wayne Bagguley)
>
> Heyd...@webtv.net (Tom McHale) wrote in message
> news:<9841-3CD...@storefull-2316.public.lawson.webtv.net>..
>
> I am aware of this background radiation but the source could be local
> even though emanating from all directions. I recall when the two Bell
> Labs employees discovered this radiation at Murray Hill. Much stronger
> evidence will be required for specific identification.
>
>
> >And what is its source? I don't want your random assertions which you
> make up in a vain attempt to rationalise you innane hypothesis. I want
> evidence, logic and reason.
>
> Somehow I don't think I'm going to get any of those from you.<
> -
> Wayne <
>
>
>
>
>
> Extraordinary claims require extraordinary evidence. Admittedly as yet I
> have no specific explanation for this background radiation except that
> it may be local, a possible combination of sources.
It is local, and inter-galactic..... it's all over the place.
>
> The big bang must be viewed in it's entirety relative to any specific
> aspect. Credulity is stretched well beyond the limits of reason by the
There is no issue of creduality, Science stands or fall pon the facts, not
your ability to digest them.
spandisman2
> Definitions:
> Micro-evolution: evolution for which the evidence is so
> overwhelming that even the ICR can't deny it.
> Macro-evolution: evolution which is only proven beyond
> reasonable doubt, not beyond unreasonable doubt.
Is this the same lack of reasonable doubt that has put numerous innocent
individuals in prison.....over the years..lol
spandisman2
"Keith[bugeye]" <marym...@earthlink.net> wrote in message
news:VnUD8.7934$Nt3.6...@newsread2.prod.itd.earthlink.net...
>
> There is no issue of creduality, Science stands or fall pon the facts, not
> your ability to digest them.
LOL, & Seems to spend more time falling than standing these days.
> > big bang. It requires more faith as does evolution than any religion
> > organized or not and of course we are all aware that faith is an
> > irrational concept. Let us be rational.
There is no such thing as a rational evolutionist, the theory, (or fact, as
they may prefer,) requires certain mental gymnastics that way surpass any
religious belief, and are verging upon the insane.
No wonder Darwin went potty.
Just look at their attitude to the rest of humanity, what a load of ignorant
arrogant anoraked tossers.
Don1
No, the majority of Americans accept the validity of evolutionary
theory. See the recent study which appears in this newsgroup in another
thread:
http://www.cnn.com/2002/TECH/science/04/30/science.understanding.ap/index.html
Were you ignorant of this data or did you knowingly tell a lie?
>
> >John D. Callahan
Wayne Bagguley
> Extraordinary claims require extraordinary evidence. Admittedly as yet I
> have no specific explanation for this background radiation except that
> it may be local, a possible combination of sources.
>
> The big bang must be viewed in it's entirety relative to any specific
> aspect.
What does that piece of verbal diarrhoea mean?
> Credulity is stretched well beyond the limits of reason by the
> big bang.
It's only your personal incredulity that's the problem.
> It requires more faith as does evolution than any religion
> organized or not
Are you claiming that there are levels of faith? Please tell me
the definition of faith you are using and how you measure the
various levels of it.
> and of course we are all aware that faith is an
> irrational concept.
So I can presume that you don't have any faith then?
> Let us be rational.
I am being rational. You are the one who is being irrational. You state
quite clearly that you "have no specific explanation for this background
radiation except that it may be local, a possible combination of sources".
If you have no explanation then how is it rational to conclude that it
may be local? In the total absence of any evidence, your explanation is
simply an irrational assertion based entirely on faith.
-
Wayne
Derek Stevenson
news:abps14$j5i$1...@paris.btinternet.com...
Interesting comparison.
In science, unlike in law, the verdict is automatically subject to appeal
whenever new evidence becomes available. And in science, again unlike in
law, anyone with the proper facilities is free to conduct a fresh trial of
the accused and come to a verdict of their own.
So now, it's not the same lack of reasonable doubt -- it's actually a far
higher standard.
Lilith
> > >tectonics and the Big Bang. If origins of species were not understood,
> > >science would say so,
> >
> > Not if there jobs depended on it being right.
>
> The job security of scientists is assured by current theories
> _not_ being right. If everything were fully understood, no
> scientists would be needed anymore, and we would be unemployed.
> Furthermore, showing that an established theory is _wrong_ and
> presenting a better alternative is the main road to fame and gain
> as a scientist. Just confirming old theories isn't going to get
> you a Nobel.
I've said this in other posts, too, but I don't think anyone is
listening. Scientists can get fame and fortune through one-upmanship
over one another. It's like sports (another male-dominated area). Each
"team" is an individual research lab. You don't get famous by being as
good as everyone else. You get famous by out-doing everyone else. Part
of that out-doing everyone else also often involves publishing papers
that say "So and so think this, but what I SAY here is the real
truth." Argument ensues, sometimes with dirty consequences.
The Big Bang is often thought to be "canonical science" as far as the
origins of the Universe goes. Steinhardt and Turok recently published
a paper that challenges the fundamental assumptions of the Big Bang
and presented a cyclical universe theory. Steinhard and Turok got
published in one of the biggest journals out there (Science). There
are other breaks with canonical science that don't get published IF
they don't have solid mathematical basis or a preponderance of
evidence. There are things that do get published without either a
solid mathematical basis or a lot of data. It is rarely consistent. To
say that anti-evolutionary theories are repressed because there is a
vast scientific conspiracy to save one's job is one of the silliest
forms of paranoia I've ever heard.
There is no scientific conspiracy. Our jobs are NOT dependent on
evolution. If the vast preponderance of data in favor of evolution
were to vanish overnight there would be as many jobs in science as
there was before. In fact, there would probably be more, as people
scrambled to set up the next experiment or author the next theory when
the next round of data came out.
I might also mention that evolutionary theory is challenged EVERY DAY
by scientists doing experiments. One does not need to assume evolution
is true to do an experiment in genomics, geology, biochemistry,
biology, or biophysics. Evolution is just a theory to fit ALL the data
from ALL the disparate sources into a coherent structure. There is no
other current theory that can explain all the scientific data out
there. And the data is so strong, and so repeatable (for example,
mathematical analyses of molecular evolution) that any scientist who
completely denies evolutionary theory is looked at with caution or
worse. It's a question of whether or not you deny reality, because the
hard evidence supporting evolution is a huge amount of reality.
But what happens to results that might contradict evolutionary theory?
Let's look at scientific history. Look at the development of quantum
theory in the early part of the 20th century. That was an enormous
contradiction. Planck didn't like the fact he was the "father" of
quantum theory. Einstein, himself a product of an earlier era of
physics, disliked some aspects of the quantum mechanics. But the
explosion in the development of physics cannot be underestimated. The
experimental results spoke to the theory and vice versa, and the
quantum theory developed and evolved. Suddenly there were jobs all
over the place as physicists scrambled to make sense of all the
contradictions, wrong paths, and theoretical dead ends. Nils Bohr,
for example, THRIVED on these kinds of contradictions. Contradiction
meant scientists had more theory to work out. MORE WORK! MORE JOBS! A
scientist who found repeatable solid evidence contradicting a
generally accepted theory would have their name in lights.
Heisenberg's uncertainty principle was contraversial. Bohr developed
his complementarity principle JUST to take into account the
particle/wave duality contradiction. Now, if this kind of explosion
among the debris of such a canonical science as 19th century physics
can leave such a fertile ground of famous names and seminal work, one
crack in the foundation of evolutionary theory...like the cracks in
the foundations of classical physics...is waiting for the next
scientist to come along and notice it.
> If there really were serious cracks in the foundations of evolution,
> an army of scientists would be digging away at them. Look at gravity
> -- there _are_ serious and well-known cracks in the foundations of
> gravity (concerning its relation to quantum theory), and digging at
> those crack is a major topic in theoretical physics.
Oh, yes. Scientists are MORE HAPPY with real repeatable results that
contradict established theories. It spells scientific success. It's
like striking OIL. It would mean they'd get famous, get more money to
study the contradictions. But after a while, when experiment after
experiment just supports a theory, it's kind of like walking over the
same path every day trying to discover a strange new land. Thousands
of experiments and observations have supported evolution. People do
continually try to find cracks in the foundation of evolutionary
theory, but so far, there are no cracks to dig at. :/ Personally I
would love to find some contradictions in evolutionary theory. It
would mean a fertile ground to study. I'm waiting to find some
"weirdnesses" in my genomics studies, but so far it's boringly
supportive of evolutionary theory.
Paraphrasing Isaac Asimov, "The "eureka" moments in science are not
accompanied by an "AHA!" but start off with "Hey, that's funny..."
> OTOH inventing cracks that aren't really there is not good
> for your job security.
If you're going to beleived to be a good scientist, you better
understand basic principles, and if you're going to claim evidence
against any theory, you better have repeatable results or a solid
mathematical proof that others can reproduce...otherwise you're lumped
into the same type of people as hypochondriacs, habitual liars, or
creation scientists. :)
By the way, the only conspiracy supporting evolution is the conspiracy
of evidence supporting it.
I'm prepared to start citing references. Are the creation scientists
ready to start debating real data?
--------------------
Deanne Taylor Ph.D.
lil...@umich.edu
Ferrous Patella
>
>
>"Keith[bugeye]" <marym...@earthlink.net> wrote in message
>news:VnUD8.7934$Nt3.6...@newsread2.prod.itd.earthlink.net...
>>
>> There is no issue of creduality, Science stands or fall pon the facts, not
>> your ability to digest them.
>
>LOL, & Seems to spend more time falling than standing these days.
For Example?
>> > big bang. It requires more faith as does evolution than any religion
>> > organized or not and of course we are all aware that faith is an
>> > irrational concept. Let us be rational.
>
>There is no such thing as a rational evolutionist, the theory, (or fact, as
>they may prefer,) requires certain mental gymnastics that way surpass any
>religious belief, and are verging upon the insane.
>No wonder Darwin went potty.
>
>Just look at their attitude to the rest of humanity, what a load of ignorant
>arrogant anoraked tossers.
>
>
4.2 on a Mark V.
Gregwrld
> It's just common sense:
>
> 1. The scientific community would not accept evolution unless it were
> tectonics and the Big Bang. If origins of species were not understood,
> singularities, time before the Big Bang, and life on other planets.
> Science is not scheming against Christians.
>
> 2. Evolution has no baring on the existence of God, because He could
> easily have created a universe complex enough to allow evolution to
> proceed by natural law. The presence and manifestation of God in the
> universe are not nullified by evolution.
>
> expanding universe, to the death of stars, to the changing chemistry
> of the Earth's atmosphere. Is life the only thing that doesn't evolve
> by natural law -- requiring the continual "tinker toying" of God?
>
> of scientists, an extensive fossil record, genetics, geology, biology,
> microevolution (laboratory and natural), and of course, common sense.
A brief perusal of the faithreason website revealed that the so-called
divinity of Jesus was supported by his "resurrection." In other words,
the claim is that because Jesus' body was not there after three days
was proof that he resurrected and was therefore a god (whatever that's
supposed to mean).
Just asking: If Joe Shmoe (perhaps my noisy next-door neighbor)died
and was buried three days ago but his body suddenly disappeared would
his relatives be able to claim divine status for him? Or would some
other conclusion seem more logical? Both the Romans and the Sanhedrin
both had good cause to see to it that the followers of Jesus not have
a rallying point in the form of Jesus' corpse. Conveniently enough,
the guard slept through it all...
The site also uses the tired arguments of Shroud of Turin advocates
while ignoring evidence for its likely status as a fraud. In short,
one could hardly recommend this site as useful support for TOE.
Greg Czebatol
Gregwrld (still waiting for evidence of creators and designers)
Adam Marczyk
news:75200cbc.02051...@posting.google.com...
Seconds, anyone?
--
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
Chris Thompson
I nominate this for Post of the Month.
I really enjoyed it. Thanks.
Chris
Bricklayer
> In article <abprns$9c8$1...@helle.btinternet.com>, spandisman2
> says...
>>
>>Just look at their attitude to the rest of humanity, what a load
>>of ignorant arrogant anoraked tossers.
>
> 4.2 on a Mark V.
>
But I really like the part about "ignorant arrogant anoraked tossers"
Brick
charlie wagner
> > Ferrous Patella wrote:
> > > In article <7a0afaa.02050...@posting.google.com>, John says...
> > > >
> > > >As a theory, evolution (Darwin) is on par with plate
> > > >tectonics and the Big Bang. If origins of species were not understood,
> > > >science would say so,
> > >
> > > Not if there jobs depended on it being right.
> >
<Snip discussion about "scientific conspiracy" and jobs>
>
> I might also mention that evolutionary theory is challenged EVERY DAY
> by scientists doing experiments. One does not need to assume evolution
> is true to do an experiment in genomics, geology, biochemistry,
> biology, or biophysics. Evolution is just a theory to fit ALL the data
> from ALL the disparate sources into a coherent structure. There is no
> other current theory that can explain all the scientific data out
> there. And the data is so strong, and so repeatable (for example,
> mathematical analyses of molecular evolution) that any scientist who
> completely denies evolutionary theory is looked at with caution or
> worse. It's a question of whether or not you deny reality, because the
> hard evidence supporting evolution is a huge amount of reality.
Let me start off by saying unequivocally that I'm not a
creationist, so you can put away any biases that you may have about
what I'm going to say. I have absolutely no religious agenda of any
kind to promote and I prefer to ignore creationist rantings and
ravings. I think that point has finally been established here to most
people's satisfaction.
That having been said, I must also start off by saying that while
I believe the evidence supports the idea that living organisms have
changed over time and the evidence also supports the idea that all
living things are related, there is not one shred of evidence of any
kind that supports any particular mechanism by which this may have
occurred. In particular, I find the neo-darwinian synthesis (or
whatever they're calling it now) to be particularly inadequate to
explain what we observe around us. While mutations do occur and while
selection can change the frequency of genes in a population, there is
no evidence that has ever been shown to me establishing a nexus
between these trivial effects and the appearance of major adaptations,
processes, structures and organisms.
So, when you say that "evolutionary theory is challenged every day
by scientists doing experiments" it makes me wonder what you mean by
"evolutionary theory" and also, what these experiments are that you're
referring to. I have never seen any evidence of any experiments that
have supported the idea that mutation and natural selection is a
mechanism that has anywhere near the creative power vested in it by
Darwin and his successors.
Perhaps you could also clarify what you mean by "evolutionary
theory". It has many faces and many aspects. Do you mean "species
change over time", or do you mean "changes in the frequencies of
alleles in a population", or do you mean "neo-darwinism" or
"ultradarwinism" (Dawkins, et.al.) or do you mean "neutral theory" or
something else?
<snip more about jobs and history>
> > If there really were serious cracks in the foundations of evolution,
> > an army of scientists would be digging away at them. Look at gravity
> > -- there _are_ serious and well-known cracks in the foundations of
> > gravity (concerning its relation to quantum theory), and digging at
> > those crack is a major topic in theoretical physics.
It looks to me like most evolutionists (as well as most cosmologists)
are out looking for more evidence to support their theory, rather than
trying to falsify it. If they were "digging away" at the flaws, this
theory would have fallen out of favor decades ago. The fact that it
still lives on is prima facie evidence that rather than trying to
falsify it, evolutionists are in a constant panic trying to figure out
ways to save it in the face of overwhelming odds. If the creationists
have done any good at all, it's been to expose this long standing hoax
that there exists a "mountain of evidence" for evolution and that
"nothing in biology would make any sense" without it. Hogwash.
> Oh, yes. Scientists are MORE HAPPY with real repeatable results that
> contradict established theories. It spells scientific success. It's
> like striking OIL. It would mean they'd get famous, get more money to
> study the contradictions. But after a while, when experiment after
> experiment just supports a theory, it's kind of like walking over the
> same path every day trying to discover a strange new land. Thousands
> of experiments and observations have supported evolution. People do
> continually try to find cracks in the foundation of evolutionary
> theory, but so far, there are no cracks to dig at. :/ Personally I
> would love to find some contradictions in evolutionary theory. It
> would mean a fertile ground to study. I'm waiting to find some
> "weirdnesses" in my genomics studies, but so far it's boringly
> supportive of evolutionary theory.
I would be more than interested in knowing what some of these
experiments are and what you think they demonstrate. What do your
"genomic studies" tell you about natural selection? What exactly do
you think the "twin nested hierarchy" means? What significance do you
attach to it? Do you think it supports a darwinian mechanism? How?
Why?
You want to find some "weirdness" in your genomic studies? There's
plenty there if you look carefully. How many genes does a yeast cell
have? Why so many? Why are the same genes used over and over in a wide
variety of species both animal and plant? Why does the gene for
hemoglobin exist in a Vicia fava genome? What do you make of adaptive
(directed) mutations? Why have some genes not changed at all over the
ages? (HOX for one) and why can a complex process like photosynthesis
be traced back to the very beginning of life on earth. On a macro
level, there are countless questionable observations that dispute
darwinism. The gaps between classes that shouldn't be there. The
sudden appearance of all of the known animal phyla in a very short
time and the appearance of no new phyla over the next 500 million
years. The fact that the fossils of the Burgess Shale and the fossils
of the Chengjiang region show no significant differences despite the
fact that they are separated in time by 40 million years, in a time
when evolution was allegedly proceeding at a very rapid rate.
Anyone who takes the time to think about this with an open mind
and just looks casually at the actual evidence cannot help but discard
this theory immediately. I don't believe in darwinism for the same
reason that I don't believe in the tooth fairy. Or god.
>
> Paraphrasing Isaac Asimov, "The "eureka" moments in science are not
> accompanied by an "AHA!" but start off with "Hey, that's funny..."
>
> > OTOH inventing cracks that aren't really there is not good
> > for your job security.
>
> If you're going to beleived to be a good scientist, you better
> understand basic principles, and if you're going to claim evidence
> against any theory, you better have repeatable results or a solid
> mathematical proof that others can reproduce...otherwise you're lumped
> into the same type of people as hypochondriacs, habitual liars, or
> creation scientists. :)
The only thing that darwinism has going for it is that it is
probably not falsifiable. Therefore, evolutionists can continue to
demand that detractors prove that it didn't happen the way
evolutionists say it did, knowing full well that this is an impossible
task. Good scientists, in my opinion, should be trying themselves to
falsify this theory. And if they had been doing their job, it would
have occurred a long time ago. Instead, everytime there is a
challenge, they simply make up a new story that explains the
discrepancies. This is not allowed in any other division of science
(except cosmology) where just so stories substitute for hard facts.
Look at Ian Musgrave's description of the evolution of the bacterial
flagellum or George Acton's desription of how the blood clotting
system evolved. It's like saying that the automobile "evolved" because
first the tires spang up, but they were used for yard swings until
they were co-opted by auto designers, and carburators sprang up, but
since there were no cars, they must have been used as door stops until
they were co-opted by auto designers for use in cars...blah, blah,
blah.
>
> By the way, the only conspiracy supporting evolution is the conspiracy
> of evidence supporting it.
To save some time, I'd be happy with just *one* piece of solid
evidence.
>
> I'm prepared to start citing references. Are the creation scientists
> ready to start debating real data?
And I'm prepared to listen to whatever you have to offer. But be
careful to produce evidence that mutation and natural selection is the
mechanism of evolution, not simply evidence that living forms changed
or that they're related.
Regards, Charlie Wagner
http://www.charliewagner.com
Adam Marczyk
news:ec838d5.02051...@posting.google.com...
This seems very peculiar in light of some of your comments below.
> there is not one shred of evidence of any
> kind that supports any particular mechanism by which this may have
> occurred. In particular, I find the neo-darwinian synthesis (or
> whatever they're calling it now) to be particularly inadequate to
> explain what we observe around us. While mutations do occur and while
> selection can change the frequency of genes in a population, there is
> no evidence that has ever been shown to me establishing a nexus
> between these trivial effects and the appearance of major adaptations,
> processes, structures and organisms.
What kind of evidence would you consider as supporting such a connection?
No, the fact that it still lives on is prima facie evidence that it is correct.
> If the creationists
> have done any good at all, it's been to expose this long standing hoax
> that there exists a "mountain of evidence" for evolution and that
> "nothing in biology would make any sense" without it. Hogwash.
How do you square this with your above statement that "I believe the evidence
supports the idea that living organisms have changed over time"? Are you now
saying the evidence does *not* support that idea?
> > Oh, yes. Scientists are MORE HAPPY with real repeatable results that
> > contradict established theories. It spells scientific success. It's
> > like striking OIL. It would mean they'd get famous, get more money to
> > study the contradictions. But after a while, when experiment after
> > experiment just supports a theory, it's kind of like walking over the
> > same path every day trying to discover a strange new land. Thousands
> > of experiments and observations have supported evolution. People do
> > continually try to find cracks in the foundation of evolutionary
> > theory, but so far, there are no cracks to dig at. :/ Personally I
> > would love to find some contradictions in evolutionary theory. It
> > would mean a fertile ground to study. I'm waiting to find some
> > "weirdnesses" in my genomics studies, but so far it's boringly
> > supportive of evolutionary theory.
>
> I would be more than interested in knowing what some of these
> experiments are and what you think they demonstrate. What do your
> "genomic studies" tell you about natural selection? What exactly do
> you think the "twin nested hierarchy" means? What significance do you
> attach to it? Do you think it supports a darwinian mechanism? How?
> Why?
> You want to find some "weirdness" in your genomic studies? There's
> plenty there if you look carefully. How many genes does a yeast cell
> have? Why so many?
The references I looked up said a yeast cell (_Saccharomyces cerevisiae_) has
4,890 genes. Why is that too many?
> Why are the same genes used over and over in a wide
> variety of species both animal and plant?
Because they were developed very early on to do very important things. Where's
the problem in that? Evolution will always use what's already available rather
than inventing new systems from scratch.
> Why does the gene for hemoglobin exist in a Vicia fava genome?
Perhaps they need it for some purpose also, and its invention predated the
animal/plant split. But more importantly - how similar is the legume hemoglobin
to vertebrate hemoglobin? The fact that they're called the same thing does not
imply that the proteins are structurally identical. A precursor organism with a
globin-like gene that then diverged into animals and plants, with each lineage
adopting the genes and diversifying them for its own purpose, is easily
compatible with evolution.
> What do you make of adaptive
> (directed) mutations?
No such thing. There are, however, some species whose mutation rates increase
under environmental stress, thus making the specific mutations they need for
survival (as well as all other mutations) more likely.
> Why have some genes not changed at all over the
> ages? (HOX for one)
Of course Hox genes have changed in various lineages. The reason they haven't
all undergone drastic change was given above: if it ain't broke, don't fix it.
> and why can a complex process like photosynthesis
> be traced back to the very beginning of life on earth.
Uh, because until there are some producers around life will only run on whatever
free, abiotically generated food is available in the environment, and that
probably wasn't much. Things didn't get off the ground until someone hit on a
way of making their own food. Why do you think this represents a problem for
evolution?
> On a macro level, there are countless questionable observations that dispute
> darwinism. The gaps between classes that shouldn't be there.
How do you square this with your above statement that "I believe the evidence
supports the idea that living organisms have changed over time"?
> The sudden appearance of all of the known animal phyla in a very short
> time and the appearance of no new phyla over the next 500 million years.
Phyla are a human classification and do not represent anything fundamental about
nature. And "all known animal phyla" did not appear in the Cambrian. Phyla have
appeared more or less constantly throughout the geologic record.
http://www.glenn.morton.btinternet.co.uk/cambevol.htm
> The fact that the fossils of the Burgess Shale and the fossils
> of the Chengjiang region show no significant differences despite the
> fact that they are separated in time by 40 million years, in a time
> when evolution was allegedly proceeding at a very rapid rate.
It was my impression that the Chengjiang fauna are not identical to those of the
Burgess Shale. Do you have evidence saying otherwise?
> Anyone who takes the time to think about this with an open mind
> and just looks casually at the actual evidence cannot help but discard
> this theory immediately. I don't believe in darwinism for the same
> reason that I don't believe in the tooth fairy. Or god.
And yet since you apparently don't deny large-scale change of life over time,
your alternative is...?
> > Paraphrasing Isaac Asimov, "The "eureka" moments in science are not
> > accompanied by an "AHA!" but start off with "Hey, that's funny..."
> >
> > > OTOH inventing cracks that aren't really there is not good
> > > for your job security.
> >
> > If you're going to beleived to be a good scientist, you better
> > understand basic principles, and if you're going to claim evidence
> > against any theory, you better have repeatable results or a solid
> > mathematical proof that others can reproduce...otherwise you're lumped
> > into the same type of people as hypochondriacs, habitual liars, or
> > creation scientists. :)
> The only thing that darwinism has going for it is that it is
> probably not falsifiable.
From a recent post of mine:
-Creatures that were a gross violation of the twin nested hierarchy; for
example, a non-primate mammal with DNA far more similar to humans than that of
the primates, or any sort of creature that appeared to "borrow" traits
horizontally across the phylogenetic tree, like whales with gills, bats with
feathers, or animals with chloroplasts in their cells. (Small segments of DNA
can sometimes jump between species through vectors like retroviruses, and
convergence does occur, but a perfect large-scale functional convergence
requiring the exact duplication of many genes would be far too unlikely for
evolution to explain.)
-Creatures that otherwise fit into the nested hierarchy but violated one of the
fundamental universals of life. For example, if we found a species of mammal
that used RNA, or some other heretofore unknown nucleic acid, as its main
molecule of heredity rather than DNA; or a species of mammal whose genetic code
was drastically different from the only one known.
-Fossils that appeared severely out of order in the geologic record; for
example, an undisputed human fossil in strata dating back to before the
emergence of mammals.
> Therefore, evolutionists can continue to
> demand that detractors prove that it didn't happen the way
> evolutionists say it did, knowing full well that this is an impossible
> task. Good scientists, in my opinion, should be trying themselves to
> falsify this theory. And if they had been doing their job, it would
> have occurred a long time ago. Instead, everytime there is a
> challenge, they simply make up a new story that explains the
> discrepancies.
You really have given us no reason at all to think this. Since you accuse
evolutionists of inventing "just-so stories", what is your alternative model,
and what hard evidence do you have that supports it?
> This is not allowed in any other division of science
> (except cosmology) where just so stories substitute for hard facts.
> Look at Ian Musgrave's description of the evolution of the bacterial
> flagellum or George Acton's desription of how the blood clotting
> system evolved. It's like saying that the automobile "evolved" because
> first the tires spang up, but they were used for yard swings until
> they were co-opted by auto designers, and carburators sprang up, but
> since there were no cars, they must have been used as door stops until
> they were co-opted by auto designers for use in cars...blah, blah,
> blah.
Apparently you don't have any objection to these scenarios other than that you
don't like them.
> > By the way, the only conspiracy supporting evolution is the conspiracy
> > of evidence supporting it.
>
> To save some time, I'd be happy with just *one* piece of solid
> evidence.
There's plenty out there. Go and look.
> > I'm prepared to start citing references. Are the creation scientists
> > ready to start debating real data?
>
> And I'm prepared to listen to whatever you have to offer. But be
> careful to produce evidence that mutation and natural selection is the
> mechanism of evolution, not simply evidence that living forms changed
> or that they're related.
Since all the work already done in this area apparently doesn't satisfy you, how
about you first tell us what you would accept as evidence for this.
Bobby D. Bryant
> To
> say that anti-evolutionary theories are repressed because there is
> a vast scientific conspiracy to save one's job is one of the
> silliest forms of paranoia I've ever heard.
Yeah, but it's a convenient belief for those whose Bronze Age
mythology has been refuted by science and who want an "explanation"
for that fact that does not require them to admit that their Bronze
Age mythology is wrong.
Bobby Bryant
Austin, Texas
Tom McHale
Re: Evolution for Dummies and Christians
snow...@snowbird.freeserve.co.uk (Wayne Bagguley)
Heyd...@webtv.net (Tom McHale) wrote in message
news:<28050-3CE...@storefull-2315.public.lawson.webtv.net>...
Extraordinary claims require extraordinary evidence. Admittedly as yet I
have no specific explanation for this background radiation except that
it may be local, a possible combination of sources.
The big bang must be viewed in it's entirety relative to any specific
aspect.
>What does that piece of verbal diarrhoea mean? <
It means that you cannot arbitrarily attribute a phenomenon to suit the
purposes of your desired conclusions.
Credulity is stretched well beyond the limits of reason by the big bang.
>It's only your personal incredulity that's the problem<.
Prove all things. I stole this from the Bible.
It requires more faith as does evolution than any religion organized or
not
>Are you claiming that there are levels of faith? Please tell me the
definition of faith you are using and how you measure the various levels
of it.<
I take very good care of my two Suburbans with emphasis on items of
safety especially the brakes therefore when I apply the brakes, I have
faith that the vehicle will stop. You might call this rational faith but
then again that is a rather blatant contradiction in terms so let us
call it rational expectations, sounds like a very good title for a movie
Now for the more commonly accepted definition of faith as exemplified
by a brown baby floating down the Nile, the precursor to Charlton
Heston, his descendent who went into business for himself and did quite
well, a delusional, ranting, hallucinating camel jockey, based on the
preceding, my faith meter registers zero.
and of course we are all aware that faith is an irrational concept.
>So I can presume that you don't have any faith then? <
Only as clearly expressed by the above paragraph.
Let us be rational.
>I am being rational. You are the one who is being irrational. You state
quite clearly that you "have no specific explanation for this background
radiation except that it may be local, a possible combination of
sources"
If you have no explanation then how is it rational to conclude that it
may be local? In the total absence of any evidence, your explanation is
simply an irrational assertion based entirely on faith. <
-
Wayne <
I have not stated localization as a fact, I am speculating 'theorizing'
and I have clearly stated this fact. And I also do not have what I would
consider a complete viable theory of quantum gravity however I am making
progress. Stay tuned.
wf...@ptd.net
(charlie wagner) wrote:
> That having been said, I must also start off by saying that while
>I believe the evidence supports the idea that living organisms have
>changed over time and the evidence also supports the idea that all
>living things are related, there is not one shred of evidence of any
>kind that supports any particular mechanism by which this may have
>occurred.
i guess charlie hasnt been paying attention to folks like francis
ayala who, at his UC Irvine webpage says his work on fruit flies has
almost resulted in speciation.
never let it be said the pedantic will let their propaganda be swayed
by facts.
>
>It looks to me like most evolutionists (as well as most cosmologists)
>are out looking for more evidence to support their theory, rather than
>trying to falsify it.
of course, there's always another scientist waiting in the wings to
prove HIS theory. charlie kind of forgets that generally there are
several theories competing to explain the same set of data. more data
generally settles the issue. if charlie were telling the truth (and
far be it from me to suggest he is), science would make no progress.
>>
>> If you're going to beleived to be a good scientist, you better
>> understand basic principles, and if you're going to claim evidence
>> against any theory, you better have repeatable results or a solid
>> mathematical proof that others can reproduce...otherwise you're lumped
>> into the same type of people as hypochondriacs, habitual liars, or
>> creation scientists. :)
> The only thing that darwinism has going for it is that it is
>probably not falsifiable.
as i said above, tell it ayala.
Therefore, evolutionists can continue to
>demand that detractors prove that it didn't happen the way
>evolutionists say it did, knowing full well that this is an impossible
>task. Good scientists, in my opinion, should be trying themselves to
>falsify this theory. And if they had been doing their job, it would
>have occurred a long time ago. Instead, everytime there is a
>challenge, they simply make up a new story that explains the
>discrepancies. This is not allowed in any other division of science
>(except cosmology) where just so stories substitute for hard facts.
hmmm i guess charlie doesnt know alot about physics...i. i. rabi's
comment about a newly discovered subatomic particle ('who ordered
THAT?') along with its attendant revision of atomic theory showed that
scientists of all disciplines modify theories to account for new
discoveries.
but lets not stand in charlie's way while he pours the cesspool of
ideology into the wading pond of science.
>Look at Ian Musgrave's description of the evolution of the bacterial
>flagellum or George Acton's desription of how the blood clotting
>system evolved. It's like saying that the automobile "evolved" because
>first the tires spang up, but they were used for yard swings until
>they were co-opted by auto designers, and carburators sprang up, but
>since there were no cars, they must have been used as door stops until
>they were co-opted by auto designers for use in cars...blah, blah,
>blah.
my GOD what a brilliant riposte!! yes, i can see it now... quantum
theory CANT be true because 'blah blah blah'...
spandisman2
"Derek Stevenson" <derekste...@yahoo.com> wrote in message
news:abr1dn$khnr0$1...@ID-139629.news.dfncis.de...
LOL, the same higher standards that gave us thalidomide no doubt, plus
numerous other scientific disasters.
By the way I agree that these are the highest standards that may be
possible, ,( human greed and lust for fame being the exceptions,) as they
deal with human life, ,, death and deformity are the alternatives.
Unfortunately they don't even begin to apply where evolutionary science is
concerned.
So basically don't expect any standards at all, no one is going to live or
die because of evolutionary beliefs, and there arn't going to be any
inquests with relatives and the general public screaming for blood and
facts.
Which as history has shown is just about the only way you'll ever get
anywhere near the real truth for anything.
cats...@yahoo.com
No, the "higher standards" are the ones that recognized very quickly
that there were unusual birth defects and identified the cause. You
are confusing the uses of the products of science with the knowledge
that is science.
> By the way I agree that these are the highest standards that may be
>possible, ,( human greed and lust for fame being the exceptions,) as they
>deal with human life, ,, death and deformity are the alternatives.
I suppose there is a sentence in there struggling to get out . . .
>Unfortunately they don't even begin to apply where evolutionary science is
>concerned.
Is the "they" you are referring to the "higher standards" Derek
refered to? If so, how do they not apply to evolution?
>So basically don't expect any standards at all, no one is going to live or
>die because of evolutionary beliefs, and there arn't going to be any
>inquests with relatives and the general public screaming for blood and
>facts.
Hmm, I wonder if the lynching victims in the South felt that way?
>Which as history has shown is just about the only way you'll ever get
>anywhere near the real truth for anything.
I'll take intelligent people, highly motivated to come up with the
best explanation and having, literally, as much time as needed, any
day.
---------------
J. Pieret
---------------
A concise definition of legal ethics:
" . . . having been bought a lawyer is supposed to stay bought."
-- Louann Miller --
Lilith
There are many mechanisms for the link between these trivial effects
and the de-novo (innovative) creation of new genes. I'm particularly
intrigued by segmental duplication as a means to generate new
chromosomal material. Segmental duplications have been shown to result
in rapid gene innovation within the great apes (This is not simple
exon shuffling.)
See for example the following reviews:
Samonte RV, Eichler EE.
Segmental duplications and the evolution of the primate genome.
Nat Rev Genet. 2002 Jan;3(1):65-72. Review.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11823792&dopt=Abstract
Eichler EE.
Recent duplication, domain accretion and the dynamic mutation of the
human genome.
Trends Genet. 2001 Nov;17(11):661-9. Review.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11672867&dopt=Abstract
> So, when you say that "evolutionary theory is challenged every day
> by scientists doing experiments" it makes me wonder what you mean by
> "evolutionary theory" and also, what these experiments are that you're
> referring to. I have never seen any evidence of any experiments that
> have supported the idea that mutation and natural selection is a
> mechanism that has anywhere near the creative power vested in it by
> Darwin and his successors.
Have you been following the scientific literature in the last few
years (not to mention the last 20 years)?
Here's a handful of very recent papers that would have different
results if evolutionary theory was different from what was expected.
That is to say, either a test of evolutionary theory in these papers
is implicit or explicit:
-------------
Mol Biol Evol 2002 May;19(5):728-35
Genome Evolution and Developmental Constraint in Caenorhabditis
elegans.
Castillo-Davis CI, Hartl DL.
Department of Organismic and Evolutionary Biology, Harvard
University.
"It has been hypothesized that evolutionary changes will be more
frequent in later ontogeny than early ontogeny because of
developmental constraint. To test this hypothesis, a genomewide
examination of molecular evolution through ontogeny was carried out
using comparative genomic data in Caenorhabditis elegans and
Caenorhabditis briggsae. We found that the mean rate of amino acid
replacement is not significantly different between genes expressed
during and after embryogenesis. However, synonymous substitution rates
differed significantly between these two classes. A genomewide survey
of correlation between codon bias and expression level found codon
bias to be significantly correlated with mRNA expression (r(s) = -0.30
and P < 10(-131)) but does not alone explain differences in dS between
classes. Surprisingly, it was found that genes expressed after
embryogenesis have a significantly greater number of duplicates in
both the C. elegans and C. briggsae genomes (P < 10(-20) and P <
10(-13)) when compared with early-expressed and nonmodulated genes. A
similarity in the distribution of duplicates of nonmodulated and
early-expressed genes, as well as a disproportionately higher number
of early pseudogenes, lend support to the hypothesis that this
difference in duplicate number is caused by selection against gene
duplicates of early-expressed genes, reflecting developmental
constraint. Developmental constraint at the level of gene duplication
may have important implications for macroevolutionary change"
--------------------------
Mol Biol Evol 2002 May;19(5):654-63
Evolution of the Phosphoglycerate mutase Processed Gene in Human and
Chimpanzee Revealing the Origin of a New Primate Gene.
Betran E, Wang W, Jin L, Long M.
Department of Ecology and Evolution, The University of Chicago.
Department of Environmental Health, University of Cincinnati.
Processed genes are created by retroposition from messenger RNA of
expressed genes. The estimated amount of processed copies of genes in
the human genome is 10,000-14,000. Some of these might be pseudogenes
with the expected pattern for nonfunctional sequences, but some others
might be an important source of new genes. We have studied the
evolution of a Phosphoglycerate mutase processed gene (PGAM3)
described in humans and believed to be a pseudogene. We sequenced
PGAM3 in chimpanzee and macaque and obtained polymorphism data for
human coding region. We found evidence that PGAM3 likely produces a
functional protein, as an example of addressing functionality for
human processed pseudogenes. First, the open reading frame was intact
despite many deletions that occurred in the 3' untranslated region.
Second, it appears that the gene is expressed. Finally, interspecies
and intraspecies variation for PGAM3 was not consistent with the
neutral model proposed for pseudogenes, suggesting that a new
functional primate gene has originated. Amino acid divergence was
significantly higher than synonymous divergence in PGAM3 lineage,
supporting positive selection acting in this gene. This role of
selection was further supported by the excess of rare alleles in a
population genetic analysis. PGAM3 is located in a region of very low
recombination; therefore, it is conceivable that the rapid fixation
events in this newly arising gene may have contributed to a selective
sweep of variation in the region.
===========================
Nature 2002 Feb 28;415(6875):1022-4
Adaptive protein evolution in Drosophila.
Smith NG, Eyre-Walker A.
Centre for the Study of Evolution and School of Biological Sciences,
University of Sussex, Brighton BN1 9QG, UK.
For over 30 years a central question in molecular evolution has been
whether natural selection plays a substantial role in evolution at the
DNA sequence level. Evidence has accumulated over the last decade that
adaptive evolution does occur at the protein level, but it has
remained unclear how prevalent adaptive evolution is. Here we present
a simple method by which the number of adaptive substitutions can be
estimated and apply it to data from Drosophila simulans and D. yakuba.
We estimate that 45% of all amino-acid substitutions have been fixed
by natural selection, and that on average one adaptive
substitution occurs every 45 years in these species.
===============================
: Proc Natl Acad Sci U S A 2002 Jan 22;99(2):862-7
Evidence for positive selection and population structure at the human
MAO-A gene.
Gilad Y, Rosenberg S, Przeworski M, Lancet D, Skorecki K.
Department of Molecular Genetics and the Crown Human Genome Center,
The Weizmann Institute of Science, Rehovot 76100, Israel.
yoav....@weizmann.ac.il
We report the analysis of human nucleotide diversity at a genetic
locus known to be involved in a behavioral phenotype, the monoamine
oxidase A gene. Sequencing of five regions totaling 18.8 kb and
spanning 90 kb of the monoamine oxidase A gene was carried out in 56
male individuals from seven different ethnogeographic groups. We
uncovered 41 segregating sites, which formed 46 distinct haplotypes. A
permutation test detected substantial population structure in these
samples. Consistent with differentiation between populations, linkage
disequilibrium is higher than expected under panmixia, with no
evidence of a decay with distance. The extent of linkage
disequilibrium is not typical of nuclear loci and suggests that the
underlying population structure may have been accentuated by a
selective sweep that fixed different haplotypes in different
populations, or by local adaptation. In support of this suggestion, we
find both a reduction in levels of diversity (as measured by a
Hudson-Kreitman-Aguade test with the DMD44 locus) and an excess of
high frequency-derived variants, as expected after a recent episode of
positive selection.
==================================
> Perhaps you could also clarify what you mean by "evolutionary
> theory". It has many faces and many aspects. Do you mean "species
> change over time", or do you mean "changes in the frequencies of
> alleles in a population", or do you mean "neo-darwinism" or
> "ultradarwinism" (Dawkins, et.al.) or do you mean "neutral theory" or
> something else?
I mean evolutionary theory as it stands in general consenus today,
beginning with natural selection, species change over time (both
gradual and punc/eek), and molecular basis for evolution that is
sometimes referred to as various different labels, depending on whom
you ask. I really could say that all of these various brands of
evolutionary theory are being tested by various people all the time.
Go to PubMed and type in "evolution". You'll get over 50,000
references. Some of them are certainly spurious, but a solid
proportion of them will address biological evolution. I say this in
order to make the point that there are many people from various
backgrounds interested in the subject.
> <snip more about jobs and history>
>
> > > If there really were serious cracks in the foundations of evolution,
> > > an army of scientists would be digging away at them. Look at gravity
> > > -- there _are_ serious and well-known cracks in the foundations of
> > > gravity (concerning its relation to quantum theory), and digging at
> > > those crack is a major topic in theoretical physics.
>
> It looks to me like most evolutionists (as well as most cosmologists)
> are out looking for more evidence to support their theory, rather than
> trying to falsify it. If they were "digging away" at the flaws, this
> theory would have fallen out of favor decades ago. The fact that it
> still lives on is prima facie evidence that rather than trying to
> falsify it, evolutionists are in a constant panic trying to figure out
> ways to save it in the face of overwhelming odds. If the creationists
> have done any good at all, it's been to expose this long standing hoax
> that there exists a "mountain of evidence" for evolution and that
> "nothing in biology would make any sense" without it. Hogwash.
Like I said above, there are over 50,000 papers that come up when you
do a search on "evolution" in PubMed, which is a limited resource to
be sure (since it often only covers the past 10 or 15 years). I would
call the greater part of 50K recent references to be mountainous. Care
to discuss any of the data?
I should put up a tutorial on how to do genomic sequence analysis for
a layperson. The tools and the data to do all of it are FREE on the
internet. That way you can generate your own mountain of data whenever
you want and not rely on what other people say to draw your own
conclusions. :)
> > Oh, yes. Scientists are MORE HAPPY with real repeatable results that
> > contradict established theories. It spells scientific success. It's
> > like striking OIL. It would mean they'd get famous, get more money to
> > study the contradictions. But after a while, when experiment after
> > experiment just supports a theory, it's kind of like walking over the
> > same path every day trying to discover a strange new land. Thousands
> > of experiments and observations have supported evolution. People do
> > continually try to find cracks in the foundation of evolutionary
> > theory, but so far, there are no cracks to dig at. :/ Personally I
> > would love to find some contradictions in evolutionary theory. It
> > would mean a fertile ground to study. I'm waiting to find some
> > "weirdnesses" in my genomics studies, but so far it's boringly
> > supportive of evolutionary theory.
>
> I would be more than interested in knowing what some of these
> experiments are and what you think they demonstrate. What do your
> "genomic studies" tell you about natural selection? What exactly do
> you think the "twin nested hierarchy" means? What significance do you
> attach to it? Do you think it supports a darwinian mechanism? How?
> Why?
I'd love to type at you at length about what I do and how I do it, but
I work for a company, so I can't give you details. I'd get in trouble.
I can tell you that I use the following principles daily with great
success:
1) Find a protein in the human genome that has no apparent "relatives"
in the human genome, for which we'd like a relative to study. Go into
more distantly related organisms (mouse, rat, worm, fly, yeast, etc)
and find the "ancestral" or divergent version of this gene by using
mathematical comparisons of sequence similarity. Then use this
ancestral/diverged gene to go back into the human sequences and use
it to find these structural relatives that are hard to find otherwise.
Apparently the original gene I need to find relatives for had split
off from the distantly related ancestor at some point, and by using
the distantly related ancestor or divergent gene I'm able to find more
distantly related homologs. There are formal programs that can make
use of this method, one popular one is called "PSI-BLAST". Can you
explain this effect outside of assuming it's due to a distantly
related ancestor gene?
2) Align two distantly related genomes together in areas of similarity
to find gene structures that are otherwise invisible by simple
examination alone. For instance, line up an area of the mouse genome
that shows a strong synteny to the human genome around a particular
gene fragment. Most of the genetic material around the gene is very
divergent (not very similar), but there are patches of the genomes
that when compared between mouse and human appear about 80% similar.
These islands of simliarity turn out to be very important areas, many
times I've seen "hidden" pieces of genes. I've found more than one
"hidden" part of a gene by doing this analysis. Mouse and human
genomes are similiar enough in these evolutionarily conserved areas to
let me easily pick out the signal from the noise *because* these
proteins specifically conserve function within the coding gene. Can
you describe this effect without using evolution? Why would mouse and
human genomes vary so much except JUST in the areas where they code
for functional protein, and then the similarity usually shoots up
above 80%?
I3) Three-dimensional conservation of protein structures between
organisms used to prove that a sequence without a solved crystal
structure has the same function (threading). It's getting late, here.
If you're interested, I can expound on this later. I want to move on
down the post.
> You want to find some "weirdness" in your genomic studies? There's
> plenty there if you look carefully. How many genes does a yeast cell
> have? Why so many?
Let's move to the literature again, for the benefit of everyone...
---------------
How many protein-coding genes are there in the Saccharomyces
cerevisiae genome?
Mackiewicz P, Kowalczuk M, Mackiewicz D, Nowicka A, Dudkiewicz M,
Laszkiewicz A, Dudek MR, Cebrat S.
Institute of Microbiology, Wroclaw University, ul. Przybyszewskiego
63/77, 51-148 Wroclaw, Poland.
"We have compared the results of estimations of the total number of
protein-coding genes in the Saccharomyces cerevisiae genome, which
have been obtained by many laboratories since the yeast genome
sequence was published in 1996. We propose that there are 5300-5400
genes in the genome. This makes the first estimation of the number of
intronless ORFs longer than 100 codons, based on the features of the
set of genes with phenotypes known in 1997 to be correct. This
estimation assumed that the set of the first 2300 genes with known
phenotypes was representative for the whole set of protein-coding
genes in the genome. The same method used in this paper for the
approximation of the total number of protein-coding sequences among
more than 40 000 ORFs longer than 20 codons gives a result that is
only slightly higher. This suggests that there are still some
non-coding ORFs in the databases and a few dozen small ORFs, not yet
annotated, which probably code for proteins."
-----------------------
I'd like to know how you are classifying 5400 genes as "so many".
Yeast cells in the wild have to be able to respond to a huge
compliment of environmental conditions. Care to tell me why it
wouldn't be advantageous for them to have a gene to code proteins for:
heat shock, different sugar receptors, different amino acid receptors,
sex selection events, asexual reproduction, and the entire compliment
of structural and biochemical proteins? 5400 is a VERY SMALL
compliment. I've always throught there should be more than that. But I
suppose yeast finds 5400 as "just right".
> Why are the same genes used over and over in a wide
> variety of species both animal and plant?
The same genes? How do you classify "same", here? Because through the
organisms, there are orthologs, but they're rarely identical. But if
you assume a common ancestor to both animal and plant, say, in the
single-cell era, then there's no problem imagining why.
>Why does the gene for hemoglobin exist in a Vicia fava genome?
Actually, it's not hemoglobin. It's leghaemoglobin. It's different.
Again, let's go to the literature (the link is at
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=protein&list_uids=126237&dopt=GenPept)
-------------------
REFERENCE 1 (residues 1 to 143)
AUTHORS Richardson,M., Dilworth,M.J. and Scawen,M.D.
TITLE The amino acid sequence of leghaemoglobin I from root
nodules of
broad bean (Vicia faba L.)
JOURNAL FEBS Lett. 51 (1), 33-37 (1975)
MEDLINE 75131397
REMARK SEQUENCE.
TISSUE=Root nodules
COMMENT [FUNCTION] Provides oxygen to the bacteroids. This role is
essential for symbiotic nitrogen fixation.
[SUBUNIT] MONOMER.
[TISSUE SPECIFICITY] Root nodules.
[MISCELLANEOUS] 4-ASP, 5-GLN, 22-GLY, 23-GLY, 34-LYS,
41-GLY,
59-GLN, 64-GLN, 71-GLU, 74-ILE, 77-GLN, 126-GLU, 128-ILE,
AND
134-GLU WERE ALSO FOUND IN THIS POOLED PREPARATION.
[SIMILARITY] BELONGS TO THE LEGHEMOGLOBIN FAMILY.
----------------------------------
There you go. Hope that helped. Note it belongs to the family. Doesn't
mean it IS hemoglobin, there.
> What do you make of adaptive
> (directed) mutations? Why have some genes not changed at all over the
> ages? (HOX for one)
Directed mutations? I think they confer an advantage. Look at HIV.
Some genes don't change because they have a selective advantage in
staying as they are. Why is that somehow not consistent with
evolution?
Which HOX? There are several different HOX genes, some of which in
the HOX genes, too. That's not exactly a really good argument against
evolution, there.
I also don't mean to sound too smarmy, here, but genes ARE conserved
between organisms. That's how we suspect we've got common ancestry.
But there are many genes which aren't in genomes like yeast or mouse
that we humans have. I can name several genes that are
primate-specific. Phorbolins 1, 2, 3, MORPHEUS, several HOX genes...
But...let's go to the data! Let's pick one homeobox gene...you're
welcome to pick any. I'll randomly choose one, HOXB4. There are
several known orthologs cross-species to HOXB4 that are called HOXB4
in each species. Hopefully, if the classification scheme works,
they'll all resemble one another discernably so we can see that they
do derive from an ancestral gene. Here's the breakdown (and you can
see the info at the following link:
http://www.ncbi.nlm.nih.gov/cgi-bin/UniGene/clust?ORG=Hs&CID=126666
Here's the similarities to the following protein:
H.sapiens: pir:T46446 - T46446 hypothetical protein DKFZp434G0128.1
250 aa
M.musculus: pir:A31757 - HOMEOBOX PROTEIN HOX-B4 95 % / 250 aa
R.norvegicus: pir:I65197 - I65197 hox1.3 protein - rat (fragment) 44 %
/ 197 aa
A.thaliana: pir:T06291 - T06291 extensin homolog T9E8.80 - Arabidopsis
thaliana 49 % / 74 aa
C.elegans: sp:P34684 - LI39_CAEEL HOMEOBOX PROTEIN LIN-39 67 % / 81 aa
D.melanogaster: pir:A26638 - HOMEOTIC DEFORMED PROTEIN 80 % / 89 aa
It doesn't look like it's consistently conserved through the animal
kingdom, does it?
> and why can a complex process like photosynthesis
> be traced back to the very beginning of life on earth.
That's not even a tough one to answer. We all apparently have the same
metabolic toolbox from that point in time, too. Where else, but in a
billion years of a population of rapidly reproducing and highly
competitive microorganisms would you get the opportunity to evolve
life as we know it? I rather like to imagine that hemoglobin, and most
of the porphyrins, stemmed out of some form of ancient chlorophyll
ancestor. It's funny how similar chlorophyll, hemoglobin, and
cobolamine are in structure and mechanism, and how they're different.
>On a macro
> level, there are countless questionable observations that dispute
> darwinism. The gaps between classes that shouldn't be there.
Such as? Give me some specifics, here.
> The
> sudden appearance of all of the known animal phyla in a very short
> time and the appearance of no new phyla over the next 500 million
> years.
Someone could remind you here that the fossil record is necessarily
incomplete. But I don't have to do that, do I?
>The fact that the fossils of the Burgess Shale and the fossils
> of the Chengjiang region show no significant differences despite the
> fact that they are separated in time by 40 million years, in a time
> when evolution was allegedly proceeding at a very rapid rate.
Define "no significant difference", and I'd like some scientific
references, please.
> Anyone who takes the time to think about this with an open mind
> and just looks casually at the actual evidence cannot help but discard
> this theory immediately. I don't believe in darwinism for the same
> reason that I don't believe in the tooth fairy. Or god.
I beleive in darwinism because I play with its consequences every day.
I suppose I could have an "open mind" and be ready to accept any other
theory that comes along, but Darwinism is how I, and the company I do
research for, gets results (see above methods for a small smattering).
>
> >
> > Paraphrasing Isaac Asimov, "The "eureka" moments in science are not
> > accompanied by an "AHA!" but start off with "Hey, that's funny..."
> >
> > > OTOH inventing cracks that aren't really there is not good
> > > for your job security.
> >
> > If you're going to beleived to be a good scientist, you better
> > understand basic principles, and if you're going to claim evidence
> > against any theory, you better have repeatable results or a solid
> > mathematical proof that others can reproduce...otherwise you're lumped
> > into the same type of people as hypochondriacs, habitual liars, or
> > creation scientists. :)
> The only thing that darwinism has going for it is that it is
> probably not falsifiable. Therefore, evolutionists can continue to
> demand that detractors prove that it didn't happen the way
> evolutionists say it did, knowing full well that this is an impossible
> task. Good scientists, in my opinion, should be trying themselves to
> falsify this theory.
They DO. Read my original post again.
>And if they had been doing their job, it would
> have occurred a long time ago.
> Instead, everytime there is a
> challenge, they simply make up a new story that explains the
> discrepancies. This is not allowed in any other division of science
> (except cosmology) where just so stories substitute for hard facts.
I think mathematical analysis of genomes, proteins, and other kinds of
analysis stand on their own:
=====================
Res Microbiol 2002 Apr;153(3):125-30 Related Articles, Books, LinkOut
New views on fungal evolution based on DNA markers and the fossil
record.
Redecker D.
Institute of Botany, University of Basel, Switzerland.
Molecular markers have facilitated a better understanding of the
evolution of fungi. Molecular phylogenetics determined the closest
relatives of fungi and defined natural groups within the true fungi.
The impact of molecular markers on the population biology of fungi has
been enormous, helping to define cryptic species and elucidating
fungal breeding biology. The interaction between molecular
phylogenetics and the fungal fossil record is discussed.
======================
Nature 2002 Apr 18;416(6882):726-9
Using the fossil record to estimate the age of the last common
ancestor of extant primates.
Tavare S, Marshall CR, Will O, Soligo C, Martin RD.
Department of Biological Sciences, University of Southern California,
Los Angeles, California 90089-1340, USA. sta...@usc.edu
Divergence times estimated from molecular data often considerably
predate the earliest known fossil representatives of the groups
studied. For the order Primates, molecular data calibrated with
various external fossil dates uniformly suggest a mid-Cretaceous
divergence from other placental mammals, some 90 million years (Myr)
ago, whereas the oldest known fossil primates are from the basal
Eocene epoch (54-55 Myr ago). The common ancestor of primates should
be earlier than the oldest known fossils, but adequate quantification
is needed to interpret possible discrepancies between molecular and
palaeontological estimates. Here we present a new statistical method,
based on an estimate of species preservation derived from a model of
the diversification pattern, that suggests a Cretaceous last common
ancestor of primates, approximately 81.5 Myr ago, close to the initial
divergence time inferred from molecular data. It also suggests that no
more than 7% of all primate species that have ever existed are known
from fossils. The approach unites all the available palaeontological
methods of timing evolutionary events: the fossil record, extant
species and clade diversification models.
==========================================
> Look at Ian Musgrave's description of the evolution of the bacterial
> flagellum or George Acton's desription of how the blood clotting
> system evolved. It's like saying that the automobile "evolved" because
> first the tires spang up, but they were used for yard swings until
> they were co-opted by auto designers, and carburators sprang up, but
> since there were no cars, they must have been used as door stops until
> they were co-opted by auto designers for use in cars...blah, blah,
> blah.
So what? How about producing some actual data to argue against,
instead of someone's explanation for evolution? REAL SCIENCE ANALYSES
DATA. You seem to be critiquing other people's explanations of the
science, not the science itself.
> > By the way, the only conspiracy supporting evolution is the conspiracy
> > of evidence supporting it.
>
> To save some time, I'd be happy with just *one* piece of solid
> evidence.
I gave you a few up above. I suppose you could reduce them all
absurdly to "circumstantial" but if you resort to that, I hold that
you will never be convinced one way or another.
> > I'm prepared to start citing references. Are the creation scientists
> > ready to start debating real data?
>
> And I'm prepared to listen to whatever you have to offer. But be
> careful to produce evidence that mutation and natural selection is the
> mechanism of evolution, not simply evidence that living forms changed
> or that they're related.
Read Eichler's segmental duplication articles above, if you can get
them. He shows the appearence of neurological genes unique to primates
which then diverge with strong evidence of positive selection. He also
shows that this kind of positive selection is apparent in what
evolutionists consider the strongest candidates for rapid evolution:
reproductive genes, xenobiotic genes, and predator/prey competition
genes. This, of course, is only one example. But you really have to
take the time to read the articles to understand the implications of
genetic-material swapping wholesale among the chromosomes.
If you can't believe this kind of smoking gun, you can't ever be
convinced, unless you can actually provide the readers with a
classification or explanation of something that would convince you.
Brian O'Neill
"Lilith" <lil...@umich.edu> wrote in message
news:75200cbc.02051...@posting.google.com...
Chris Ho-Stuart
all kinds of concrete examples of applications of biological
evolution.
The message Id of the nominated article is
<75200cbc.02051...@posting.google.com>
Lilith <lil...@umich.edu> wrote:
> cha...@charliewagner.com (charlie wagner) wrote in message news:<ec838d5.02051...@posting.google.com>...
[snip 592 lines of detailed and specific responses on applications
I'm leaving in just the conclusion]
>> And I'm prepared to listen to whatever you have to offer. But be
>> careful to produce evidence that mutation and natural selection is the
>> mechanism of evolution, not simply evidence that living forms changed
>> or that they're related.
>
> Read Eichler's segmental duplication articles above, if you can get
> them. He shows the appearence of neurological genes unique to primates
> which then diverge with strong evidence of positive selection. He also
> shows that this kind of positive selection is apparent in what
> evolutionists consider the strongest candidates for rapid evolution:
> reproductive genes, xenobiotic genes, and predator/prey competition
> genes. This, of course, is only one example. But you really have to
> take the time to read the articles to understand the implications of
> genetic-material swapping wholesale among the chromosomes.
>
> If you can't believe this kind of smoking gun, you can't ever be
> convinced, unless you can actually provide the readers with a
> classification or explanation of something that would convince you.
>
>>
>> Regards, Charlie Wagner
>> http://www.charliewagner.com
>>
>> >
>> > --------------------
>> > Deanne Taylor Ph.D.
>> > lil...@umich.edu
>
> --------------------
> Deanne Taylor Ph.D.
> lil...@umich.edu
Cheers -- Chris
Brian O'Neill
"Chris Ho-Stuart" <host...@sky.fit.qut.edu.au> wrote in message
news:3ce2...@news.qut.edu.au...
Sverker Johansson
>
> I already nominated it, but I'll second yours...
>
> "Chris Ho-Stuart" <host...@sky.fit.qut.edu.au> wrote in message
> news:3ce2...@news.qut.edu.au...
> > I nominate this for POTM; it would be a useful resource for finding
> > all kinds of concrete examples of applications of biological
> > evolution.
> >
> > The message Id of the nominated article is
> > <75200cbc.02051...@posting.google.com>
> >
> > Lilith <lil...@umich.edu> wrote:
[snip nominated post]
[snip also Charlie's illustration of my .sig]
Lilith has two posts in this thread nominated now -- can we put
them jointly on a single ballot for POTM?
--
Best regards, HLK, Physics
Sverker Johansson U of Jonkoping
----------------------------------------------
Rodjk
> POTM Nominee
Seconded!!
(Sorry Louanne:-(
Rodjk #613
Lilith
for the yeast genome paper in the parent post (likely due to my
middle-of-the-night cutting and pasting skills).
Here it is in full:
Yeast 2002 May;19(7):619-629 [epub ahead of print]
Copyright 2002 John Wiley & Sons, Ltd.
PMID: 11967832 [PubMed - as supplied by publisher]
lil...@umich.edu (Lilith) wrote in message news:<75200cbc.02051...@posting.google.com>...
>
>
Adam Marczyk
> Brian O'Neill wrote:
> >
> > I already nominated it, but I'll second yours...
> >
> > "Chris Ho-Stuart" <host...@sky.fit.qut.edu.au> wrote in message
> > news:3ce2...@news.qut.edu.au...
> > > I nominate this for POTM; it would be a useful resource for finding
> > > all kinds of concrete examples of applications of biological
> > > evolution.
> > >
> > > The message Id of the nominated article is
> > > <75200cbc.02051...@posting.google.com>
> > >
> > > Lilith <lil...@umich.edu> wrote:
>
> [snip nominated post]
>
> [snip also Charlie's illustration of my .sig]
>
> Lilith has two posts in this thread nominated now -- can we put
> them jointly on a single ballot for POTM?
That sounds like a good idea to me.
Dunno
On Wed, 15 May 2002, Rodjk wrote:
> "Brian O'Neill" <bria...@prodigy.net> wrote in message news:<2unE8.40132$G%3.182...@typhoon.columbus.rr.com>...
> > POTM Nominee
>
> Seconded!!
> (Sorry Louanne:-(
>
Another MOTP (Month Of The Posts) in the making.
-
Today is Setting Orange, the 62nd day of Discord in the YOLD 3168
.
Derek Stevenson
> "Derek Stevenson" <derekste...@yahoo.com> wrote in message
> news:abr1dn$khnr0$1...@ID-139629.news.dfncis.de...
> > "spandisman2" <pl...@noddynet.com> wrote in message
> > news:abps14$j5i$1...@paris.btinternet.com...
> > > Is this the same lack of reasonable doubt that has put numerous
> innocent
> > > individuals in prison.....over the years..lol
> >
> > Interesting comparison.
> >
> > In science, unlike in law, the verdict is automatically subject to
appeal
> > whenever new evidence becomes available. And in science, again unlike
in
> > law, anyone with the proper facilities is free to conduct a fresh trial
of
> > the accused and come to a verdict of their own.
> >
> > So now, it's not the same lack of reasonable doubt -- it's actually a
far
> > higher standard.
>
> LOL, the same higher standards that gave us thalidomide no doubt, plus
> numerous other scientific disasters.
No, the same standards that were *disregarded* in the case of thalidomide.
Nice try, though. Perhaps you'd like to:
a) point out where it is written that science should be capable of
delivering answers with Absolute Certainty; and
b) share with us some of these "numerous other scientific disasters".
Oh, and while you're at it -- the same standards are at work in the
determination that stepping into the path of a speeding truck is not
conducive to one's continued good health. Please feel free to demonstrate
consistency in your rejection of these standards.
> By the way I agree that these are the highest standards that may be
> possible, ,( human greed and lust for fame being the exceptions,) as
they
> deal with human life, ,, death and deformity are the alternatives.
> Unfortunately they don't even begin to apply where evolutionary science
is
> concerned.
Huh?
> So basically don't expect any standards at all, no one is going to live
or
> die because of evolutionary beliefs,
Never heard of antibiotic-resistant bacteria?
> and there arn't going to be any
> inquests with relatives and the general public screaming for blood and
> facts.
> Which as history has shown is just about the only way you'll ever get
> anywhere near the real truth for anything.
You were just complaining about "numerous innocent individuals in prison".
You don't suppose that "relatives and the general public screaming for
blood and facts" could have had anything to do with those cases, do you?
charlie wagner
I am familiar with the work being done in the Eichler lab and others,
including Susan Rosenberg at Baylor. People are beginning to look at
the genome a little bit differently now, and that's good. The "hoops
of steel" that bound us to the darwinian paradigm are being loosened
and gradually a new paradigm is emerging, one in which the genome is
seem in a more dynamic and adaptive light. Those who insist on
clinging to the old paradigm and who continue to try to shoehorn these
new discoveries into the old molds will be left behind. But it's a
little like what we heard in the 60's about civil rights. The people
said that "these things take time, we can't change decades of behavior
in one day. Be patient" And so it is in science. You can't change
deeply ingrained thought patterns over night and you have to expect a
lot of resistance from the "statics" who insist on clinging to past
dogma. Those who want to be at the head of the train, the leaders, not
the followers, are plunging foward into a new understanding of the
genome and how it works. It's going to be an exciting time ahead, and
I only wish I was young again so I could look foward to it.
The Eichler lab states:
"The long-term goal of our laboratory is to understand the
evolution, pathology and mechanism(s) of recent gene duplication and
DNA transposition within the human genome. Our research specifically
addresses a new paradigm that has emerged in the past few years
regarding the dynamic nature of human genome structure. Particular
chromosomal regions have been shown to be active in the acquisition,
duplication and dispersal of large gene-containing genomic segments.
We hypothesize that these ?jumping genomic segments? are part of an
ongoing evolutionary process that results in a novel form of
large-scale variation in human genomic DNA and contributes rapidly to
primate gene evolution. The large blocks of sequence similarity
generated by this process, we further propose, provide the substrates
for aberrant recombination, thereby leading to recurrent and
potentially pathogenic chromosomal structural rearrangements."
Barbara McClintock said in her Nobel laureate address "the genome
is a highly sensitive organ of the cell, that in times of stress could
initiate it's own restructuring and renovation". A far cry from the
concept of random, fortuitous mutations.
James Shapiro has made the bold statement that "cells can engineer
their own genomes", and Susan Rosenberg states "the emerging
mechanisms of adaptive genetic change cast evolution, development and
heredity into a new perspective, indicating new models for the genetic
changes that fuel these processes".
And as these folks uncover more of the details, the darwinian
paradigm falls farther and farther behind. No evidence of any kind has
yet been presented that these kinds of changes in the genome, from
simple point mutations to complex restructuring of large segments of
the genome can ever lead to new major adaptations, processes,
functions, structures or organisms. The evolution that we see is
trivial, and only involves minor changes. We still seem to cling to
the notion that these trivial changes can somehow lead to the creation
of complex new adapatations. We imagine that the impossible can be
made possible, if we just cut it up into small enough steps and give
it a sufficient amount of time.
> > So, when you say that "evolutionary theory is challenged every day
> > by scientists doing experiments" it makes me wonder what you mean by
> > "evolutionary theory" and also, what these experiments are that you're
> > referring to. I have never seen any evidence of any experiments that
> > have supported the idea that mutation and natural selection is a
> > mechanism that has anywhere near the creative power vested in it by
> > Darwin and his successors.
>
> Have you been following the scientific literature in the last few
> years (not to mention the last 20 years)?
Yes, and it tells me that darwinism is dead but they just don't know
how to break the news to us.
<SNIP cites>
>
> > Perhaps you could also clarify what you mean by "evolutionary
> > theory". It has many faces and many aspects. Do you mean "species
> > change over time", or do you mean "changes in the frequencies of
> > alleles in a population", or do you mean "neo-darwinism" or
> > "ultradarwinism" (Dawkins, et.al.) or do you mean "neutral theory" or
> > something else?
>
> I mean evolutionary theory as it stands in general consenus today,
> beginning with natural selection, species change over time (both
> gradual and punc/eek), and molecular basis for evolution that is
> sometimes referred to as various different labels, depending on whom
> you ask. I really could say that all of these various brands of
> evolutionary theory are being tested by various people all the time.
> Go to PubMed and type in "evolution". You'll get over 50,000
> references. Some of them are certainly spurious, but a solid
> proportion of them will address biological evolution. I say this in
> order to make the point that there are many people from various
> backgrounds interested in the subject.
There is no general consensus that I can see. It seems to me that
"evolutionary theory" is whatever the person you're asking says it is
and as you point out "all the various brands of evolutionary theory
are being tested..." So the word "evolution" has no particular
meaning at all. And there is no one particular "evolutionary theory".
I try to not make that same mistake. I don't attack "evolution"
because nobody knows what it means. I attack "darwinism", which is
still a little murky, but not as bad as "evolution" At least with
darwinism, most people know you mean something about variation and
selection. But even that is murky, because Darwin was firmly against
"leaps" and insisted that his mechanism relied on the gradual
accumulation of fortuitous variations over a very long period of time.
>
> > <snip more about jobs and history>
> >
> > > > If there really were serious cracks in the foundations of evolution,
> > > > an army of scientists would be digging away at them. Look at gravity
> > > > -- there _are_ serious and well-known cracks in the foundations of
> > > > gravity (concerning its relation to quantum theory), and digging at
> > > > those crack is a major topic in theoretical physics.
> >
> > It looks to me like most evolutionists (as well as most cosmologists)
> > are out looking for more evidence to support their theory, rather than
> > trying to falsify it. If they were "digging away" at the flaws, this
> > theory would have fallen out of favor decades ago. The fact that it
> > still lives on is prima facie evidence that rather than trying to
> > falsify it, evolutionists are in a constant panic trying to figure out
> > ways to save it in the face of overwhelming odds. If the creationists
> > have done any good at all, it's been to expose this long standing hoax
> > that there exists a "mountain of evidence" for evolution and that
> > "nothing in biology would make any sense" without it. Hogwash.
>
> Like I said above, there are over 50,000 papers that come up when you
> do a search on "evolution" in PubMed, which is a limited resource to
> be sure (since it often only covers the past 10 or 15 years). I would
> call the greater part of 50K recent references to be mountainous. Care
> to discuss any of the data?
I would like very much to discuss the data. You can start by defining
evolution for me.
>
> I should put up a tutorial on how to do genomic sequence analysis for
> a layperson. The tools and the data to do all of it are FREE on the
> internet. That way you can generate your own mountain of data whenever
> you want and not rely on what other people say to draw your own
> conclusions. :)
I'm not taking issue with genomic sequence analysis. But it's only a
baby step. Just elucidating the sequences of the bases is important
and a necessary step, but it tells us little about how the genome
functions. That undertanding will come later. We are at the stage now
where I would be if someone laid out the source code (in binary) for
Windows and I compared it to other MS products and I found similar
sections of code in other programs, or I found repeating sections of
code in the same program. It would be an interesting first step, but
would tell me little about what Windows does and what it's overall
capabilities are.
>
> > > Oh, yes. Scientists are MORE HAPPY with real repeatable results that
> > > contradict established theories. It spells scientific success. It's
> > > like striking OIL. It would mean they'd get famous, get more money to
> > > study the contradictions. But after a while, when experiment after
> > > experiment just supports a theory, it's kind of like walking over the
> > > same path every day trying to discover a strange new land. Thousands
> > > of experiments and observations have supported evolution. People do
> > > continually try to find cracks in the foundation of evolutionary
> > > theory, but so far, there are no cracks to dig at. :/ Personally I
> > > would love to find some contradictions in evolutionary theory. It
> > > would mean a fertile ground to study. I'm waiting to find some
> > > "weirdnesses" in my genomics studies, but so far it's boringly
> > > supportive of evolutionary theory.
> >
> > I would be more than interested in knowing what some of these
> > experiments are and what you think they demonstrate. What do your
> > "genomic studies" tell you about natural selection? What exactly do
> > you think the "twin nested hierarchy" means? What significance do you
> > attach to it? Do you think it supports a darwinian mechanism? How?
> > Why?
>
> I'd love to type at you at length about what I do and how I do it, but
> I work for a company, so I can't give you details. I'd get in trouble.
>
> I can tell you that I use the following principles daily with great
> success:
>
<snip desription of Dr. Taylor's work>
It sounds like very interesting work, and I sometimes regret that I
didn't continue on in my research career, but with a family to
support, I opted to serve mammon. :-)
>
>
> > You want to find some "weirdness" in your genomic studies? There's
> > plenty there if you look carefully. How many genes does a yeast cell
> > have? Why so many?
>
<snip cites>
>
> I'd like to know how you are classifying 5400 genes as "so many".
> Yeast cells in the wild have to be able to respond to a huge
> compliment of environmental conditions. Care to tell me why it
> wouldn't be advantageous for them to have a gene to code proteins for:
> heat shock, different sugar receptors, different amino acid receptors,
> sex selection events, asexual reproduction, and the entire compliment
> of structural and biochemical proteins? 5400 is a VERY SMALL
> compliment. I've always throught there should be more than that. But I
> suppose yeast finds 5400 as "just right".
OK, I thought the number was closer to 6000. It's silly to try to
argue how many is too many, or too few. It has what it has. I just
personally find it just a little odd that it has so many. Of course,
the question to ask is "where did all those genes come from?" Do you
have any ideas about that?
>
> > Why are the same genes used over and over in a wide
> > variety of species both animal and plant?
>
> The same genes? How do you classify "same", here? Because through the
> organisms, there are orthologs, but they're rarely identical. But if
> you assume a common ancestor to both animal and plant, say, in the
> single-cell era, then there's no problem imagining why.
I find the fact that the same genes are used over and over again to be
a fact of profound significance. It tells me that genes didn't
"evolve" at all, that they have some other, unknown origin, and
they're transferred and used as building blocks for organisms.
I have to stop here. I'll post this and try to get to the rest later.
charlie wagner
<snip part of message previously replied to>
>
> Which HOX? There are several different HOX genes, some of which in
> the HOX genes, too. That's not exactly a really good argument against
> evolution, there.
>
> I also don't mean to sound too smarmy, here, but genes ARE conserved
> between organisms. That's how we suspect we've got common ancestry.
> But there are many genes which aren't in genomes like yeast or mouse
> that we humans have. I can name several genes that are
> primate-specific. Phorbolins 1, 2, 3, MORPHEUS, several HOX genes...
>
> But...let's go to the data! Let's pick one homeobox gene...you're
> welcome to pick any. I'll randomly choose one, HOXB4. There are
> several known orthologs cross-species to HOXB4 that are called HOXB4
> in each species. Hopefully, if the classificion scheme works,
> they'll all resemble one another discernably so we can see that they
> do derive from an ancestral gene. Here's the breakdown (and you can
> see the info at the following link:
>
> http://www.ncbi.nlm.nih.gov/cgi-bin/UniGene/clust?ORG=Hs&CID=126666
>
> Here's the similarities to the following protein:
> H.sapiens: pir:T46446 - T46446 hypothetical protein DKFZp434G0128.1
> 250 aa
>
> M.musculus: pir:A31757 - HOMEOBOX PROTEIN HOX-B4 95 % / 250 aa
> R.norvegicus: pir:I65197 - I65197 hox1.3 protein - rat (fragment) 44 %
> / 197 aa
> A.thaliana: pir:T06291 - T06291 extensin homolog T9E8.80 - Arabidopsis
> thaliana 49 % / 74 aa
> C.elegans: sp:P34684 - LI39_CAEEL HOMEOBOX PROTEIN LIN-39 67 % / 81 aa
> D.melanogaster: pir:A26638 - HOMEOTIC DEFORMED PROTEIN 80 % / 89 aa
>
> It doesn't look like it's consistently conserved through the animal
> kingdom, does it?
OK, here's the rub, as they say. There is no question at all that all
living organisms are closely related. On a cellular level, there is
little difference from the one to another WRT the biochemistry,
replication, cell division, cellular respiration, etc. From a genomic
standpoint, the same genes are used again and again across a wide
range of species. Often times these genes are slightly different but
they still function in a similar fashion. So, I'm not surprised at all
that there is an 80% similarity between H. sapiens and D. melanogaster
and a 95% similarity between H. sapiens and M. musculus.
The question is, what does this *mean*? What is the significance
of this observation? And more to the point, what does it say about
evolution? You use words and phrases like "conserved" and "common
ancestor", which have evolutionary implications. They suggest that
genes "evolved" from other genes by a mechanism that consists of
random mutations and/or other types of random processes such as
recombination and drift and were "conserved" because they had a high
selective value. I maintain that we don't know the origin of genes at
all, and we can't say that they came to be by a darwinian mechanism of
evolution. In fact we can't say anything at all about the origin of
the genes. They could just have well come to the earth from elsewhere
already containing the information that they use or they just as well
may have been generated by other genomes by some sort of unfolding of
an algorithm that was already present. Evolutionists are seeing
"relatedness" and they are automatically assuming an evolutionary
explanation. And this may well be because they are working from the
premise that "evolutionary theory" is correct and therefore they may
be explaining everything they see in the light of that pre-existing
bias, rather than as new data. The fact is, IMHO, the fact that all
living organisms are closely related is of profound significance, but
that it says nothing whatsoever about their origins or their possible
evolution. The only two things that we know for sure are that all
living organisms are related and that the organisms that lived in the
past are different from those that are extant today. Everything else
is a deep mystery. But not knowing the origin of life doesn't mean we
can't know how it works. The research that is being conducted is
important research, not so much because it can solve the mystery of
our origins, but because by knowing how everything works, helps us to
control and transcend it.
>
>
> > and why can a complex process like photosynthesis
> > be traced back to the very beginning of life on earth.
>
> That's not even a tough one to answer. We all apparently have the same
> metabolic toolbox from that point in time, too. Where else, but in a
> billion years of a population of rapidly reproducing and highly
> competitive microorganisms would you get the opportunity to evolve
> life as we know it? I rather like to imagine that hemoglobin, and most
> of the porphyrins, stemmed out of some form of ancient chlorophyll
> ancestor. It's funny how similar chlorophyll, hemoglobin, and
> cobolamine are in structure and mechanism, and how they're different.
Yes, I was astonished myself when I first examined the chemical
structure of hemoglobin and chlorophyll. In fact, in the old days :-)
I was one of the only people in my group to champion the work of Lynn
Margulis when people were saying she was a crackpot. I always had a
strong attraction to the radical thinkers and the crackpots. They are
often the source of the best thinking. You can put that example under
my list of "weirdnesses". Anyway, I think it's pretty clear (to me
anyway) that photosynthesis didn't 'evolve" here on earth from the
primordal ooze. Rather, I think it's highly likely that it came to
earth from elsewhere already to go. The oldest stromatolites go back
at least 3.45 billion years. That doesn't give very much time for it
to evolve. But just look at those molecules. The argument from
incredulity makes a very strong case that this is no accident.
>
> >On a macro
> > level, there are countless questionable observations that dispute
> > darwinism. The gaps between classes that shouldn't be there.
>
> Such as? Give me some specifics, here.
Well, I don't want to get into a whole thing about transitional forms,
that's a bottomless pit if ever there was one. Suffice it to say that
the fossil record tells us almost nothing about the evolutionary
origin of phyla and classes. Intermediate forms are non-existent,
undiscovered or not recognized. Ask any paleontologist.
>
> > The
> > sudden appearance of all of the known animal phyla in a very short
> > time and the appearance of no new phyla over the next 500 million
> > years.
>
> Someone could remind you here that the fossil record is necessarily
> incomplete. But I don't have to do that, do I?
After 142 years of looking by plenty of grad students and post-docs,
one would expect that at least one example of *most* extinct forms
would have been found. A large percentage for sure. There are god
knows how many millions of living forms, I don't know the number
exactly, we have far fewer extinct forms represented than extant
forms. It ought to be the other way around, shouldn't it?
>
> >The fact that the fossils of the Burgess Shale and the fossils
> > of the Chengjiang region show no significant differences despite the
> > fact that they are separated in time by 40 million years, in a time
> > when evolution was allegedly proceeding at a very rapid rate.
>
> Define "no significant difference", and I'd like some scientific
> references, please.
"Fossilized Soft-bodied Fauna", Chen Jun-Yuan, Jan Bergstrom and Hou
Xiangguang
National Geographic Research and Exploration, Winter 1991
An exerpt from his conclusion:
"In fact, evolutionarily, the Chengjiang arthropods
are not much different from those of the Burgess Shale, despite their
distinctly older age, and, hence, do not bring us much closer to the
origin
of arthropods, at least not from a morphological point of view.
Part of the importance of the Chengjiang fauna mav lie in the
implication
that the initial coelomate radiation was extremely rapid and
morphologically far-reaching. The Middle Cambrian Burgess Shale fauna
shows several of the animal phyla we meet in the seas today.
A step back in time some tens of millions of years brings us to the
Early
Cambrian Chengjiang fauna. During this time span, evolution seems to
have produced very little change."
>
> > Anyone who takes the time to think about this with an open mind
> > and just looks casually at the actual evidence cannot help but discard
> > this theory immediately. I don't believe in darwinism for the same
> > reason that I don't believe in the tooth fairy. Or god.
>
> I beleive in darwinism because I play with its consequences every day.
> I suppose I could have an "open mind" and be ready to accept any other
> theory that comes along, but Darwinism is how I, and the company I do
> research for, gets results (see above methods for a small smattering).
Darwinism is a mechanism, based on variation and selection. There is
no question that mutations occur and there is no question that
selection can change the frequencies of alleles in populations. What
is lacking is evidence that these trivial effects can produce major
adaptive changes, new structures and processes and new organisms. With
all due respect, and feel free to correct me if I'm wrong, it would
appear to me that this question regarding the creative power of
darwinism is not something that enters into your daily activities.
>
>
> >
> > >
> > > Paraphrasing Isaac Asimov, "The "eureka" moments in science are not
> > > accompanied by an "AHA!" but start off with "Hey, that's funny..."
When I got married in 1965, I moved out of my house and took my
own place. My mother, in her usual fashion, threw out everything that
I had left behind which she deemed to be "junk". Among that stuff was
my proudest possession, a letter from Isaac Asimov that I received in
reply to a query about flying saucers. He lambasted me for being such
an idiot and reminded me that only a complete moron could ever believe
in flying saucers. Later, in the middle 70's I attended the National
Science Teachers Convention in Chicago and there were two keynote
speakers on the same day. Sagan in the morning and Asimov in the
afternoon! After the talk, I engaged Asimov in conversation and told
him the story. He found it amusing and took my address, saying he
would write another note for me. He never did. But I felt terrific
about the conversation, especially the part where he remembered my
father's candy store on Kings Highway in Brooklyn.
Now, if you're looking for weirdness, here's an adult portion.
Why should the molecular data show divergence times that considerably
pre-date the paleontological record? One of them is wrong. You'll
probably argue that the fossil record is incomplete and these forms
are out there waiting to be discovered, but my money is on the fossil
record. I think this is clear evidence that we're not actually seeing
what we think we're seeing when we look at the molecular data.
> ==========================================
>
> > Look at Ian Musgrave's description of the evolution of the bacterial
> > flagellum or George Acton's desription of how the blood clotting
> > system evolved. It's like saying that the automobile "evolved" because
> > first the tires spang up, but they were used for yard swings until
> > they were co-opted by auto designers, and carburators sprang up, but
> > since there were no cars, they must have been used as door stops until
> > they were co-opted by auto designers for use in cars...blah, blah,
> > blah.
>
> So what? How about producing some actual data to argue against,
> instead of someone's explanation for evolution? REAL SCIENCE ANALYSES
> DATA. You seem to be critiquing other people's explanations of the
> science, not the science itself.
I'd like to see some actual data to show that variation and selection
have anywhere near the creative power vested in them. So far, it's
just a story, a leap of faith and simply unbelievable. Scientists have
some nerve demanding that detractors come up with hard evidence to
demonstrate that evolution didn't happen the way they say it did when
they themselves have produced not a smidgen of data to show that it
has.
>
> > > By the way, the only conspiracy supporting evolution is the conspiracy
> > > of evidence supporting it.
> >
> > To save some time, I'd be happy with just *one* piece of solid
> > evidence.
>
> I gave you a few up above. I suppose you could reduce them all
> absurdly to "circumstantial" but if you resort to that, I hold that
> you will never be convinced one way or another.
The evidence you offer reinforces the already accepted notion that all
living organisms are related and that changes can occur in genomes by
a variety of methods. What your evidence does not estanblish, is a
nexus between changes in the frequencies of alleles in populations
under selection pressure, and new major adaptations.
>
> > > I'm prepared to start citing references. Are the creation scientists
> > > ready to start debating real data?
> >
> > And I'm prepared to listen to whatever you have to offer. But be
> > careful to produce evidence that mutation and natural selection is the
> > mechanism of evolution, not simply evidence that living forms changed
> > or that they're related.
>
> Read Eichler's segmental duplication articles above, if you can get
> them. He shows the appearence of neurological genes unique to primates
> which then diverge with strong evidence of positive selection. He also
> shows that this kind of positive selection is apparent in what
> evolutionists consider the strongest candidates for rapid evolution:
> reproductive genes, xenobiotic genes, and predator/prey competition
> genes. This, of course, is only one example. But you really have to
> take the time to read the articles to understand the implications of
> genetic-material swapping wholesale among the chromosomes.
Do you really believe for a second that the higher neurological
function found in the human brain, the complex and subtle ability to
make abstractions and to solve problems, the musical and artistic
ability, the language skills and the emotions were the product of
random fortuitous errors in the genomes and selection pressure? You
might as well believe that the moon is made of green cheese.
>
> If you can't believe this kind of smoking gun, you can't ever be
> convinced, unless you can actually provide the readers with a
> classification or explanation of something that would convince you.
Nothing, I'm afraid, will ever convince me that evolution proceeds at
the direction of random, fortuitous mutations and natural selection.
Sorry.
Ian Musgrave & Peta O'Donohue
Address altered to avoid spam, delete RemoveInsert
Piggybacking
On Wed, 15 May 2002 00:24:14 +0000 (UTC), wf...@ptd.net wrote:
>On Tue, 14 May 2002 19:12:52 +0000 (UTC), cha...@charliewagner.com
>(charlie wagner) wrote:
[snip]
>>Look at Ian Musgrave's description of the evolution of the bacterial
>>flagellum or George Acton's desription of how the blood clotting
>>system evolved. It's like saying that the automobile "evolved" because
>>first the tires spang up, but they were used for yard swings until
>>they were co-opted by auto designers, and carburators sprang up, but
>>since there were no cars, they must have been used as door stops until
>>they were co-opted by auto designers for use in cars...blah, blah,
>>blah.
[snip]
<SIGH> As I have said before, using human built machines as an analogy
to biological systems can lead one profoundly astray. Co-opting a
hollow stlyette that secretes materials distant to the bacterial cell
as a rotating hollow stylette that propells the cell as well as
secreting things far from the cell is in no way analagous to the steps
Mr. Wagner proposes (and can be done relatively simply from modest
changes to a Tol/Pal like transporter).
I mean a metabolic enzyme was co-opted as a lens protein, that's like
co-opting an electric motor as a window. If natura can do that, why is
a flagella so hard to imagine?
Cheers! Ian
=====================================================
Ian Musgrave Peta O'Donohue,Jack Francis and Michael James Musgrave
reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
Southern Sky Watch http://www.abc.net.au/science/space/default.htm
Lilith
> lil...@umich.edu (Lilith) wrote in message news:<75200cbc.02051...@posting.google.com>...
> > and the de-novo (innovative) creation of new genes. I'm particularly
> > intrigued by segmental duplication as a means to generate new
> > chromosomal material. Segmental duplications have been shown to result
> > in rapid gene innovation within the great apes (This is not simple
> > exon shuffling.)
> >
> > See for example the following reviews:
> >
> > Samonte RV, Eichler EE.
>> Segmental duplications and the evolution of the primate genome.
> > Nat Rev Genet. 2002 Jan;3(1):65-72. Review.
> > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11823792&dopt=Abstract
> >
> > Eichler EE.
> > Recent duplication, domain accretion and the dynamic mutation of the
> > human genome.
> > Trends Genet. 2001 Nov;17(11):661-9. Review.
> > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11672867&dopt=Abstract
> >
>
> I am familiar with the work being done in the Eichler lab and others,
> including Susan Rosenberg at Baylor. People are beginning to look at
> the genome a little bit differently now, and that's good. The "hoops
> of steel" that bound us to the darwinian paradigm are being loosened
> and gradually a new paradigm is emerging, one in which the genome is
> seem in a more dynamic and adaptive light.
I'm still failing to see where the fusion between genetic adaptation,
environmental pressure, and Darwininan selection can result in a "new
paradigm". Nothing that's come out of recent genetic analysis has put
any strain on Darwinian adaptation and selection. To the contrary,
it's *supportive* of it.
But let me go into the specifics of Eichler's work, as an
illustration. (I should be clear on Eichler's results, here for those
not familiar with his work). All quotes are from the Eichler/Samote
paper referenced above. Bracketed [] insertions inside quotes are
mine.
1) Segmental duplication is where small swaths of DNA are copied from
one area of a chromosome and either deposited somewhere on the same
chromosome or inserted into another chromosome:
"Segmental duplications are large, nearly identical
copies of genomic DNA, which range in
size from 1 to >200 kb and are present in at
least two locations [chromosomal structural locations -- not
individual locations --d] in the human genome."
Sometimes there are genes there already when the entire area is copied
into another chromosome. In fact, in these duplicated areas, there is
evidence for many superposed duplication events within this
"innovative" areas of the genome but not so many duplications outside
of the innovative areas into the older more "staid" collections of
genes. But when there is evidence for the occasional seg dup outside
the hot spots, they have been shown to be linked to some genetic
diseases, including infertility and Williams-Beuren syndrome.
As for that "structural location" I noted in the quote, Eichler found
that within the chromosomes of the great apes there is evidence that
the "central area" of each chromosome (100MB around each centromere)
is a hot
region of cross-chromosomal segmental duplication and there are some
chromosomes which show more of this kind of duplication than others.
INTERESTINGLY, one of the hot spots is...and some of you already are
suspecting this -- the Y chromosome, which will make some
selectionists say "Aha!":
"Their [segmental duplications] high sequence identity
(90?100%) provides ample substrate for
paralogous recombination events to occur
and they have been identified on every
human chromosome. The distribution of
these segments among human chromosomes
seems non-uniform (TABLE 1), with some
chromosomes, such as the Y chromosome,
showing peculiar enrichments for these types
of duplication."
Within the duplicating regions one can examine the genetic material to
see how it diverges between the parent site and the site where it was
deposited. Eichler was able to show that there are many of these
duplicated regions that ONLY show in the "old world" primates alive
today, and there are even duplicated regions only found in the
chimp/man line.
"Attempts to reconstruct the evolutionary history of several
segmental duplications show high levels of
restructuring of primate chromosomes over
the past 35 million years. Differences in copy
number and location of duplicated segments
have been observed for many chromosomes,
particularly between the genomes of man and
the great apes. The effects, as expected,
are most pronounced in regions near centromeres
and telomeres,where accelerated
rates of duplication and rearrangement
have markedly altered the structure between
species and in populations."
The Samonte/Eichler conclusion on the mechanism of seg dup is
therefore,
"This continuum of segmental duplication
events during recent primate evolutionary
history is generally supported by in silico
analysis of the human genome, which has
used the sequence divergence of the duplicated
segments to estimate their evolutionary
age. Both interchromosomal and intrachromosomal
duplications that range from 90 to
100% sequence identity have been identified,
indicating that segmental duplication has
been a continuing process during the past 35
million years of evolution (FIG. 3). Overall,
these studies indicate that segmental duplications
have subtly and consistently restructured
primate chromosomes (although possibly
not at a constant rate) during evolution."
2) Eichler then examined the genes structures that appear inside these
primate-specific segmental duplications. As expected, there are many
"dead" genes within the duplicated regions:
"From the perspective of the gene, there are
several potential consequences of recent segmental
duplications. The most likely outcome
is that the duplicated genomic segment
that harbours intron and exon structure is
non-functional, which leads to the accumulation
of unprocessed pseudogenes1.Most of
the duplicated regions in the human genome
are littered with the ?carcasses? of paralogous
copies with no apparent function."
Eichler then goes on to point out that many of these beasties are
STILL transcribed into mRNA, though they're shuffled and strangely
spliced, and probably not functional on all evidence thus far.
Eichler then focused on one particular gene within one type of
segmental duplication originating from Chromsome 16:
"Rapid evolution of primate genes has also
been documented for interspersed segmental
duplications. A 20-kb segment of chromosome
16, termed LCR16a, recently (12?
Mya) proliferated, creating 15?30 copies that
are dispersed throughout 15 Mb of the short
arm of human and chimpanzee chromosome
16."
One gene seemed to be replicated within this example, throughout one
particular instance of this seg dup copies....
A novel hominoid gene family (termed
morpheus, after the Greek god of dreams who
could change into many different human
forms) was discovered in half of the human
duplicates. Surprisingly, the exonic regions of
this gene family showed accelerated rates of
mutation when compared with intronic
regions (FIG. 5)."
I believe that when I saw Eichler present this data at RECOMB he noted
morpheus as a brain-specific protein, which is interesting. Morpheus
is clearly a hominid-specific gene and change has been positively
selected for:
"Comparison of putative protein-
encoding exons revealed that most of
these changes [mutations] (>95%) resulted in amino-acid
changes. Consequently, average coding
sequence divergence (15?20%) among copies
between human and chimpanzee far exceeds
the amount of intronic sequence divergence
(1?2%)."
Since the "neutral" areas of the genome -- the non-coding areas -- in
the region of these duplications are mutating at 1-2% divergence rate
between chimps and humans, and the protein-coding (functional) area of
this protein is mutating at a much faster rate (20% divergence) then,
therefore, the changes in the functional regions are *selected for*.
"Analysis of this gene family among
hominoids shows that the main episode of
enhanced amino-acid replacement occurred
after the separation of human, chimpanzee
and gorilla lineages from the orang-utans (30-
fold accelerated rate of amino-acid replacement
when compared with neutrally
evolving DNA)."
Not only were these genes replicated, but were also changed up through
the primate lineage.
"The second important lesson learned from
LCR16a amplification is that the evolution
of this duplication was accompanied
strong POSITIVE SELECTION. Unlike most other
examples of gene duplication, there is no evidence
from the morpheus gene family for
conservation of ancestral function. In fact, the
genic segments in many respects seem to have
evolved from the ?ether? of non-functional
DNA or DNA under weak NEGATIVE SELECTION".
How is that possible? Eichler posits the fact that once these genes
take foothold in a population, they're advantageous enough that they
spread rapidly through a population, or are selected for through
sexual selection (as has been observed in other studies).
The Samonte/Eichler final conclusion is:
"The organization and architecture of segmental
duplications have two very broad
implications in our understanding of the evolution
and function of our genome. Particular
regions of the genome have experienced extraordinary
rates of evolutionary turnover,which
result in considerable structural change
between closely related primate species. This
finding challenges our rather static idea of primate
chromosomal evolution on the basis of
cytogenetic data and indicates that non-uniform
rates of genomic mutation might exist."
A discovery of a mechanism for gene innovation will also possibly help
explain why primates were able to "accelerate" into a greater
intellectual capacity.
This next conclusion should not be under-estimated. The implications
for these findings are enormous. They actually point to the mechanism
by which primates are distinguished from other animals.
"Second, the process provides the opportunity
for the duplication and transposition of genes
into new chromosomal environments that
allows them to evolve unencumbered by selective
constraint. The recent origin of segmental
duplications provides an ample substrate for
both the alteration of existing genes and the
birth of new ones. It is, therefore, not implausible
that new genes with altered functions have
emerged that distinguish man and great apes
both at the phenotypic and genotypic level."
So...
Eichler showed that some of these primate-specific areas show the
development of NEW GENES that exist nowhere else in the animal
kingdom.
There is evidence for positive selection WITHIN the genes in these
recent duplications.
The mechanisms that Eichler examines are ways for genotypes to
innovate new genes, but I've yet to see how a mechanism such as
segmental duplication contradicts Darwinism in any way. It in fact
supports it, since until Eichler took the time to examine the "genetic
fossils" within our DNA, mechanisms for innovating new genes were
unclear in the primates, at least.
Segmental duplicaiton shuffling and redistribution of genetic material
within chromosomes is a mechanism for generating new genetic material,
itself. Within the this does not somehow question the /result/ of
these mechanisms, which is diversification of genotypes which can
respond to evolutionary pressure in a more plastic and adaptable way.
> Those who insist on
> clinging to the old paradigm and who continue to try to shoehorn these
> new discoveries into the old molds will be left behind.
I don't understand why you think this needs to be "shoehorned" in. Can
you be more specific, as to exactly WHY these results go against
evidence for selection? Because the results found evidence for
selection. You don't need to shoehorn the conformation of selection
events into Darwinism.
> But it's a
> little like what we heard in the 60's about civil rights. The people
> said that "these things take time, we can't change decades of behavior
> in one day. Be patient" And so it is in science. You can't change
> deeply ingrained thought patterns over night and you have to expect a
> lot of resistance from the "statics" who insist on clinging to past
> dogma.
I think what I've been saying all along is falling on deaf ears, here.
I hope not.
I'm telling you that dogma does not get one the Nobel prize.
Scientists are chipping away at foundations all the time. Sometimes
all they reveal is new, stronger foundation.
If you think that all young scientists and students have a century's
worth of work beat into their heads when they emerge into their
professional careers...to make them some kind of robot automaton, then
CLEARLY you don't know most scientific graduate students, or you have
a ridiculous idea of what real-life people are like.
Evolution is accepted as a consensus of data. It's not a mantra that
is beat into the heads of young scientists. Evolution was mentioned as
a PASSING THING to me as I was studying chemistry, physics, and
molecular biology. "Oh, by the way, the data appears to be best fit by
the evolutionary theory we have today." I don't call that dogma.
If you came up with data that goes against evolutionary theory, and
was repeatable, you'd become famous and there would be a scramble to
try to figure it out. If you come up with data that extends
evolutionary theory, then yea, you're going to get people saying it
extends evolutionary theory. Your complaint earlier, that people just
are able to fit new data easily into evolutionary theory by positing
"made up scenarios" to fit the data begs the question...why are they
so easily able to do that? Sure, evolution should be able to be
falsifyable. It can be falsifyable in a number of various different
ways. Find an animal who survives in an environment who is not native
to that environment.
Humans are the exception because we can engineer our environments to
suit us.
> Those who want to be at the head of the train, the leaders, not
> the followers, are plunging foward into a new understanding of the
> genome and how it works. It's going to be an exciting time ahead, and
> I only wish I was young again so I could look foward to it.
> The Eichler lab states:
> "The long-term goal of our laboratory is to understand the
> evolution, pathology and mechanism(s) of recent gene duplication and
> DNA transposition within the human genome. Our research specifically
> addresses a new paradigm that has emerged in the past few years
> regarding the dynamic nature of human genome structure. Particular
> chromosomal regions have been shown to be active in the acquisition,
> duplication and dispersal of large gene-containing genomic segments.
> We hypothesize that these ?jumping genomic segments? are part of an
> ongoing evolutionary process that results in a novel form of
> large-scale variation in human genomic DNA and contributes rapidly to
> primate gene evolution. The large blocks of sequence similarity
> generated by this process, we further propose, provide the substrates
> for aberrant recombination, thereby leading to recurrent and
> potentially pathogenic chromosomal structural rearrangements."
> Barbara McClintock said in her Nobel laureate address "the genome
> is a highly sensitive organ of the cell, that in times of stress could
> initiate it's own restructuring and renovation". A far cry from the
> concept of random, fortuitous mutations.
Darwinism doesn't posit randome, fortuitous mutations. Darwin wasn't
even around when DNA was discovered. Darwin posited natural selection.
Random, fortuitous mutations ARE supported in Eichler's work on the
actual micro-structure of the segmental duplications.
> James Shapiro has made the bold statement that "cells can engineer
> their own genomes", and Susan Rosenberg states "the emerging
> mechanisms of adaptive genetic change cast evolution, development and
> heredity into a new perspective, indicating new models for the genetic
> changes that fuel these processes".
None of this speaks against natural selection.
> And as these folks uncover more of the details, the darwinian
> paradigm falls farther and farther behind.
I'm STILL failing to see how any of this goes against a darwinian
paradigm. What do you call "darwinian"? Random mutations? Darwin never
said anything of the kind. Darwin posited natural selection. The
environment chooses which genotype of the organism wins out.
The mechanisms for ESTABLISHING those genotypes which are THEN
selected for are what you and I have been talking about, here. Those
are mechanisms FOR natural selection. Those are mechanisms which allow
natural selection to occur with some "winners" at the end. You
haven't shown me how any of these mechanisms go against Darwinian
evolution.
> No evidence of any kind has
> yet been presented that these kinds of changes in the genome, from
> simple point mutations to complex restructuring of large segments of
> the genome can ever lead to new major adaptations, processes,
> functions, structures or organisms.
Maybe I should start bringing up HOX function, now. Want to talk about
how point mutations in HOX regions affects the timing of embryonic
development and actually makes morphological change apparent?
Speciation is also suggested in Eichler's work. But I skipped most of
that.
> The evolution that we see is
> trivial, and only involves minor changes. We still seem to cling to
> the notion that these trivial changes can somehow lead to the creation
> of complex new adapatations. We imagine that the impossible can be
> made possible, if we just cut it up into small enough steps and give
> it a sufficient amount of time.
We don't cling to any such idea. We have evidence for these processes.
Care to tell me how everything you've just quoted is not evidence for
what you're arguing against?
I don't call restructuring of a genome "small scale", nor do I call
the change from ape to human "small scale" at least from this end.
> > > So, when you say that "evolutionary theory is challenged every day
> > > by scientists doing experiments" it makes me wonder what you mean by
> > > "evolutionary theory" and also, what these experiments are that you're
> > > referring to. I have never seen any evidence of any experiments that
> > > have supported the idea that mutation and natural selection is a
> > > mechanism that has anywhere near the creative power vested in it by
> > > Darwin and his successors.
> >
> > Have you been following the scientific literature in the last few
> > years (not to mention the last 20 years)?
>
> Yes, and it tells me that darwinism is dead but they just don't know
> how to break the news to us.
You're kidding, right? Who is "THEY"? Honestly, Charlie, who is
"They"? There is no "they". That's purely paranoid.
> <SNIP cites>
>
>
> >
> > > Perhaps you could also clarify what you mean by "evolutionary
> > > theory". It has many faces and many aspects. Do you mean "species
> > > change over time", or do you mean "changes in the frequencies of
> > > alleles in a population", or do you mean "neo-darwinism" or
> > > "ultradarwinism" (Dawkins, et.al.) or do you mean "neutral theory" or
> > > something else?
> >
> > I mean evolutionary theory as it stands in general consenus today,
> > beginning with natural selection, species change over time (both
> > gradual and punc/eek), and molecular basis for evolution that is
> > sometimes referred to as various different labels, depending on whom
> > you ask. I really could say that all of these various brands of
> > evolutionary theory are being tested by various people all the time.
> > Go to PubMed and type in "evolution". You'll get over 50,000
> > references. Some of them are certainly spurious, but a solid
> > proportion of them will address biological evolution. I say this in
> > order to make the point that there are many people from various
> > backgrounds interested in the subject.
>
> There is no general consensus that I can see. It seems to me that
> "evolutionary theory" is whatever the person you're asking says it is
> and as you point out "all the various brands of evolutionary theory
> are being tested..." So the word "evolution" has no particular
> meaning at all. And there is no one particular "evolutionary theory".
You're right. By the strictest standard, there IS NO ONE EVOLUTIONARY
THEORY IN THE DETAILS. There is only the theory which BEST FITS THE
DATA and in the outlier details it's still hazy because there isn't
enough detail in the data yet to fill in the gaps.
> I try to not make that same mistake. I don't attack "evolution"
> because nobody knows what it means. I attack "darwinism", which is
> still a little murky, but not as bad as "evolution"
Darwinism suggests speciation through selection and divergence. Again,
I don't see how anything we've talked about here denies that.
>At least with
> darwinism, most people know you mean something about variation and
> selection. But even that is murky, because Darwin was firmly against
> "leaps" and insisted that his mechanism relied on the gradual
> accumulation of fortuitous variations over a very long period of time.
Darwin was also operating in 1850 before anyone knew anything about
genetics. But we know that.
> > > <snip more about jobs and history>
> > >
> > > > > If there really were serious cracks in the foundations of evolution,
> > > > > an army of scientists would be digging away at them. Look at gravity
> > > > > -- there _are_ serious and well-known cracks in the foundations of
> > > > > gravity (concerning its relation to quantum theory), and digging at
> > > > > those crack is a major topic in theoretical physics.
> > >
> > > It looks to me like most evolutionists (as well as most cosmologists)
> > > are out looking for more evidence to support their theory, rather than
> > > trying to falsify it. If they were "digging away" at the flaws, this
> > > theory would have fallen out of favor decades ago. The fact that it
> > > still lives on is prima facie evidence that rather than trying to
> > > falsify it, evolutionists are in a constant panic trying to figure out
> > > ways to save it in the face of overwhelming odds. If the creationists
> > > have done any good at all, it's been to expose this long standing hoax
> > > that there exists a "mountain of evidence" for evolution and that
> > > "nothing in biology would make any sense" without it. Hogwash.
> >
> > Like I said above, there are over 50,000 papers that come up when you
> > do a search on "evolution" in PubMed, which is a limited resource to
> > be sure (since it often only covers the past 10 or 15 years). I would
> > call the greater part of 50K recent references to be mountainous. Care
> > to discuss any of the data?
>
> I would like very much to discuss the data. You can start by defining
> evolution for me.
I did. Don't go pedantic on me, here. You're not going to make a
point by making me jump through hoops for you.
> > I should put up a tutorial on how to do genomic sequence analysis for
> > a layperson. The tools and the data to do all of it are FREE on the
> > internet. That way you can generate your own mountain of data whenever
> > you want and not rely on what other people say to draw your own
> > conclusions. :)
>
> I'm not taking issue with genomic sequence analysis. But it's only a
> baby step. Just elucidating the sequences of the bases is important
> and a necessary step, but it tells us little about how the genome
> functions. That undertanding will come later.
I'm not sure if I know what you mean, here. Elucidating the sequence
of the bases isn't what I'm talking about. I'm talking about
comparitive genomics.
>We are at the stage now
> where I would be if someone laid out the source code (in binary) for
> Windows and I compared it to other MS products and I found similar
> sections of code in other programs, or I found repeating sections of
> code in the same program. It would be an interesting first step, but
> would tell me little about what Windows does and what it's overall
> capabilities are.
Now you're moving from Darwinism into systems biology. What's your
point here, with systems biology? That understanding systems biology
is necessary to understand evolution? I've got more references on
comparitive systems biology if you'd like them. :)
Me too, but lucky for me I get paid to do this in these times. Which
is a good thing. :)
> >
> > I'd like to know how you are classifying 5400 genes as "so many".
> > Yeast cells in the wild have to be able to respond to a huge
> > compliment of environmental conditions. Care to tell me why it
> > wouldn't be advantageous for them to have a gene to code proteins for:
> > heat shock, different sugar receptors, different amino acid receptors,
> > sex selection events, asexual reproduction, and the entire compliment
> > of structural and biochemical proteins? 5400 is a VERY SMALL
> > compliment. I've always throught there should be more than that. But I
> > suppose yeast finds 5400 as "just right".
>
> OK, I thought the number was closer to 6000. It's silly to try to
> argue how many is too many, or too few. It has what it has. I just
> personally find it just a little odd that it has so many. Of course,
> the question to ask is "where did all those genes come from?" Do you
> have any ideas about that?
As for where the genes come from, there's a lot of conjecture. I don't
worry about where they came from. I just know how they develop through
the "family tree" from the data. When data comes around as to where
they came from, that's when I'll start peeking. :)
>
>
> >
> > > Why are the same genes used over and over in a wide
> > > variety of species both animal and plant?
> >
> > The same genes? How do you classify "same", here? Because through the
> > organisms, there are orthologs, but they're rarely identical. But if
> > you assume a common ancestor to both animal and plant, say, in the
> > single-cell era, then there's no problem imagining why.
>
> I find the fact that the same genes are used over and over again to be
> a fact of profound significance. It tells me that genes didn't
> "evolve" at all, that they have some other, unknown origin, and
> they're transferred and used as building blocks for organisms.
But they do evolve. There are genes that are clearly ancestral to
genes we have today, in Giardia, in yeast, in bacteria...genes DO
suddenly appear. That's why yeast has 5400 genes and worm has ~14000
genes and mankind has about 30,000 genes (or more)...many of these
genes are completely new constructs, though many of them have
ancestors that are apparent from sequence comparison. If these kinds
of genes can duplicate and arise through the lineage, and we can see
the same kinds of basic genes down by bacteria (which are themselves
highly evolved and at the branch tips, not the base of the tree) then
why can't we extrapolate back to an ancestral organism that had fewer
genes? I don't understand the contradiction, here. It's not dogma,
it's simple inference.
Gavin Tabor
However I just want you to know that your post found (at least) one
fascinated reader - you must have a very interesting job.
Gavin
Chris Ho-Stuart wrote:
--
Dr. Gavin Tabor
School of Engineering and Computer Science
Department of Engineering
University of Exeter
Lilith
Eichler's work can't be clearer on that subject (previous post).
>In fact we can't say anything at all about the origin of
> the genes. They could just have well come to the earth from elsewhere
> already containing the information that they use or they just as well
> may have been generated by other genomes by some sort of unfolding of
> an algorithm that was already present.
Not being able to say where genes come from is not evidence against
selection. It's lack of evidence as to the origin of genes.
> Evolutionists are seeing
> "relatedness" and they are automatically assuming an evolutionary
> explanation.
We've seen genes appear that weren't there in ancestral states. See
previous post.
> And this may well be because they are working from the
> premise that "evolutionary theory" is correct and therefore they may
> be explaining everything they see in the light of that pre-existing
> bias, rather than as new data.
That might be true if it was one experiment with one set of data. The
interesting thing is that you can assume a different subset of
assupmtions in every experiment and get confirmation of your
experiment. Add up enough of these and you get overlap. I don't see
what the problem is, here. I haven't seen any huge gaps in a consensus
evolutionary theory that can't be eventually filled in by more data as
it comes available. Selection is apparent. Genetic drift is apparent.
Etc.
I still don't see how an argument from incredulity can make any kind
of case when there's no rates, no data, no known conditions, no facts
to be incredulous against. There's no data on the ability or inability
of any of these molecules springing forth from any kind of primordial
soup. There's incredulity in both directions. In otherwords, it's
null. So to say that an argument from incredulity is a strong argument
against earthly development is selectively ignoring the other half of
the argument, in that there's equal problems with assuming that it's
not of earthly origins, and in some people's opinion, much less
possible.
> >
> > >On a macro
> > > level, there are countless questionable observations that dispute
> > > darwinism. The gaps between classes that shouldn't be there.
> >
> > Such as? Give me some specifics, here.
>
>
> Well, I don't want to get into a whole thing about transitional forms,
> that's a bottomless pit if ever there was one. Suffice it to say that
> the fossil record tells us almost nothing about the evolutionary
> origin of phyla and classes. Intermediate forms are non-existent,
> undiscovered or not recognized. Ask any paleontologist.
There are whole papers and research on transitional fossils. Which
paleontologist says there's none?
> >
> > > The
> > > sudden appearance of all of the known animal phyla in a very short
> > > time and the appearance of no new phyla over the next 500 million
> > > years.
> >
> > Someone could remind you here that the fossil record is necessarily
> > incomplete. But I don't have to do that, do I?
>
> After 142 years of looking by plenty of grad students and post-docs,
> one would expect that at least one example of *most* extinct forms
> would have been found. A large percentage for sure. There are god
> knows how many millions of living forms, I don't know the number
> exactly, we have far fewer extinct forms represented than extant
> forms. It ought to be the other way around, shouldn't it?
That's a straw man argument. You know as well as I do, if you have any
kind of scientific background, that fossils only form under specific,
specialized conditions, usually having to do with sedementary
deposits. If you die outside of a body of water or some kind of
special dessicating/preserving environment, your remains won't be
found. That's why we make such a big deal out of mummies, for
instance.
> >
> > >The fact that the fossils of the Burgess Shale and the fossils
> > > of the Chengjiang region show no significant differences despite the
> > > fact that they are separated in time by 40 million years, in a time
> > > when evolution was allegedly proceeding at a very rapid rate.
> >
> > Define "no significant difference", and I'd like some scientific
> > references, please.
>
> "Fossilized Soft-bodied Fauna", Chen Jun-Yuan, Jan Bergstrom and Hou
> Xiangguang
> National Geographic Research and Exploration, Winter 1991
>
> An exerpt from his conclusion:
>
> "In fact, evolutionarily, the Chengjiang arthropods
> are not much different from those of the Burgess Shale, despite their
> distinctly older age, and, hence, do not bring us much closer to the
> origin
> of arthropods, at least not from a morphological point of view.
> Part of the importance of the Chengjiang fauna mav lie in the
> implication
> that the initial coelomate radiation was extremely rapid and
> morphologically far-reaching. The Middle Cambrian Burgess Shale fauna
> shows several of the animal phyla we meet in the seas today.
> A step back in time some tens of millions of years brings us to the
> Early
> Cambrian Chengjiang fauna. During this time span, evolution seems to
> have produced very little change."
How does this go against evolution? There have been species who have
seen very little change over the eons. Some have appeared quite
suddenly. If you have a rich niche that doesn't require a lot of
evolutionary pressure to adapt to, then why would a species adapt?
>
>
> >
> > > Anyone who takes the time to think about this with an open mind
> > > and just looks casually at the actual evidence cannot help but discard
> > > this theory immediately. I don't believe in darwinism for the same
> > > reason that I don't believe in the tooth fairy. Or god.
> >
> > I beleive in darwinism because I play with its consequences every day.
> > I suppose I could have an "open mind" and be ready to accept any other
> > theory that comes along, but Darwinism is how I, and the company I do
> > research for, gets results (see above methods for a small smattering).
>
> Darwinism is a mechanism, based on variation and selection. There is
> no question that mutations occur and there is no question that
> selection can change the frequencies of alleles in populations. What
> is lacking is evidence that these trivial effects can produce major
> adaptive changes, new structures and processes and new organisms. With
> all due respect, and feel free to correct me if I'm wrong, it would
> appear to me that this question regarding the creative power of
> darwinism is not something that enters into your daily activities.
I view genetic diversity and development as major changes. I'll reply
more on this later as I have a 10am meeting and it's getting late. :)
Sverker Johansson
> snow...@snowbird.freeserve.co.uk (Wayne Bagguley)
> Heyd...@webtv.net (Tom McHale) wrote in message
> news:<28050-3CE...@storefull-2315.public.lawson.webtv.net>...
>
> Extraordinary claims require extraordinary evidence. Admittedly as yet I
> have no specific explanation for this background radiation except that
> it may be local, a possible combination of sources.
Elsewhere in this thread I posted references to evidence that it's
non-local.
> The big bang must be viewed in it's entirety relative to any specific
> aspect.
Exactly. Which is what you do _not_ do, when you only address single
aspects, like the CMB. Lots of separate lines of evidence all
point towards the universe as we know it having a finite history,
on the order of 14 billion years, and having been much denser and
hotter once. None of them in itself is absolutely certain proof,
but when the evidence is viewed in its entirety it is very strong
indeed.
I have yet to see you address that entirety, other than expressing
your personal incredulity. And frankly, your incredulity is
_your_ problem, not the universe's.
[snip]
Rodjk
Has the cock crowed three times yet??
> And I'm prepared to listen to whatever you have to offer. But be
> careful to produce evidence that mutation and natural selection is the
> mechanism of evolution, not simply evidence that living forms changed
> or that they're related.
Prepared to listen? HA!
Rodjk #613
Jack Dominey
> Nothing, I'm afraid, will ever convince me that evolution proceeds at
> the direction of random, fortuitous mutations and natural selection.
> Sorry.
If you really mean that, then don't ask for evidence you won't believe
anyway. Spend your time trying to find other observable mechanisms
and argue why they're superior.
Free advice, worth what you paid for it.
Jack Dominey
elvon is a spamtrap
jack_dominey (at) email (dot) com
George Acton
>
> cha...@charliewagner.com (charlie wagner) wrote in message news:<ec838d5.02051...@posting.google.com>...
> >
> > I would like very much to discuss the data. You can start by defining
> > evolution for me.
>
> I did. Don't go pedantic on me, here. You're not going to make a
> point by making me jump through hoops for you.
Clue: he has already done so. In fact, the entire thread consists
of your jumping through hoops for him. But the abstracts and
your discussion have been interestng. for third parties.
--George Acton
charlie wagner
The paradigm shift involves looking at the genome in a new way. Rather
than minimizing mutation rates and random genetic change, it appears
more likely that the genome may be able to change quickly and
substantially in such a way as to restructure and renovate itself. And
it also includes the idea that this process could be the result of the
genome itself initiating these changes rather than the result of
random, accidental occurrences. And in my view, there is simply no
room in this new paradigm for anything resembling darwinism.
>
> But let me go into the specifics of Eichler's work, as an
> illustration. (I should be clear on Eichler's results, here for those
> not familiar with his work). All quotes are from the Eichler/Samote
> paper referenced above. Bracketed [] insertions inside quotes are
> mine.
>
> 1) Segmental duplication is where small swaths of DNA are copied from
> one area of a chromosome and either deposited somewhere on the same
> chromosome or inserted into another chromosome:
>
> "Segmental duplications are large, nearly identical
> copies of genomic DNA, which range in
> size from 1 to >200 kb and are present in at
> least two locations [chromosomal structural locations -- not
> individual locations --d] in the human genome."
The "deep" question here, of course, is "why does this occur"?
And "is this a random, accidental process or is it 'guided' and
intentional"?
>
> Sometimes there are genes there already when the entire area is copied
> into another chromosome. In fact, in these duplicated areas, there is
> evidence for many superposed duplication events within this
> "innovative" areas of the genome but not so many duplications outside
> of the innovative areas into the older more "staid" collections of
> genes. But when there is evidence for the occasional seg dup outside
> the hot spots, they have been shown to be linked to some genetic
> diseases, including infertility and Williams-Beuren syndrome.
>
> As for that "structural location" I noted in the quote, Eichler found
> that within the chromosomes of the great apes there is evidence that
> the "central area" of each chromosome (100MB around each centromere)
> is a hot
> region of cross-chromosomal segmental duplication and there are some
> chromosomes which show more of this kind of duplication than others.
> INTERESTINGLY, one of the hot spots is...and some of you already are
> suspecting this -- the Y chromosome, which will make some
> selectionists say "Aha!":
What is also interesting is why there are "hot spots" at all, and why
the central region around the centromere? Some hot spots can be
stress-induced, but not all of them.
>
> "Their [segmental duplications] high sequence identity
> (90?100%) provides ample substrate for
> paralogous recombination events to occur
> and they have been identified on every
> human chromosome. The distribution of
> these segments among human chromosomes
> seems non-uniform (TABLE 1), with some
> chromosomes, such as the Y chromosome,
> showing peculiar enrichments for these types
> of duplication."
Again, their etiology is not clear. They may not be totally random, as
darwinism might suggest, but rather an important part of an overall
process that is occurring that is anything but random.
>
> Within the duplicating regions one can examine the genetic material to
> see how it diverges between the parent site and the site where it was
> deposited. Eichler was able to show that there are many of these
> duplicated regions that ONLY show in the "old world" primates alive
> today, and there are even duplicated regions only found in the
> chimp/man line.
This is interesting, but again it's significance is unknown. Since all
primates are very closely related, one would expect to find a lot of
this kind of event. But in my view it tells us nothing about the
mechanism involved, only that the genomes are closely related. It
certainly isn't any kind of evidence for a darwinian mechanism.
>
> "Attempts to reconstruct the evolutionary history of several
> segmental duplications show high levels of
> restructuring of primate chromosomes over
> the past 35 million years. Differences in copy
> number and location of duplicated segments
> have been observed for many chromosomes,
> particularly between the genomes of man and
> the great apes. The effects, as expected,
> are most pronounced in regions near centromeres
> and telomeres,where accelerated
> rates of duplication and rearrangement
> have markedly altered the structure between
> species and in populations."
I don't like his use of the phrase "evolutionary history". It's like
he already has a bias about evolution and he's using the relatedness
that he sees to support that bias. The fact is that there has been a
lot of restructuring of primate chromosomes over the past 35 million
years but I'm not able to see how this ties in with any sort of
darwinian mechanism. In fact, we don't really know what the mechanism
is, whether it's random or directed, and whether selection has played
any role in it's occurrence.
>
> The Samonte/Eichler conclusion on the mechanism of seg dup is
> therefore,
>
> "This continuum of segmental duplication
> events during recent primate evolutionary
> history is generally supported by in silico
> analysis of the human genome, which has
> used the sequence divergence of the duplicated
> segments to estimate their evolutionary
> age. Both interchromosomal and intrachromosomal
> duplications that range from 90 to
> 100% sequence identity have been identified,
> indicating that segmental duplication has
> been a continuing process during the past 35
> million years of evolution (FIG. 3). Overall,
> these studies indicate that segmental duplications
> have subtly and consistently restructured
> primate chromosomes (although possibly
> not at a constant rate) during evolution."
I would change the last sentence to read as follows:
"Overall,these studies indicate that segmental duplications have
subtly and consistently restructured primate chromosomes (although
possibly not at a constant rate) during the past 35 million years"
>
> 2) Eichler then examined the genes structures that appear inside these
> primate-specific segmental duplications. As expected, there are many
> "dead" genes within the duplicated regions:
>
> "From the perspective of the gene, there are
> several potential consequences of recent segmental
> duplications. The most likely outcome
> is that the duplicated genomic segment
> that harbours intron and exon structure is
> non-functional, which leads to the accumulation
> of unprocessed pseudogenes1.Most of
> the duplicated regions in the human genome
> are littered with the ?carcasses? of paralogous
> copies with no apparent function."
Pseudogenes are DNA sequences that resemble functional genes but seem
to have no apparent purpose. Emphasis on the word *apparent*. I don't
think it's at all clear what pseudogenes are, why they exist, whether
their occurrence is random or directed or for that matter, whether or
not they have any function. You know, when you erase a program from a
computer drive, the whole program is not erased. Usually only certain
bits are altered so the program looks like it's gone to the computer,
but the code is still there and can often be recovered. Perhaps
pseudogenes are "working code" that the genome uses in processing new
changes. We simply don't know. To say that pseudogenes have any
evolutionary significance I think, is not warranted. And to
characterize them as non-functional is likewise unwarranted.
Especially in view of the fact that we are completely ignorant as to
why they exist.
>
> Eichler then goes on to point out that many of these beasties are
> STILL transcribed into mRNA, though they're shuffled and strangely
> spliced, and probably not functional on all evidence thus far.
More "weirdness", huh?
>
> Eichler then focused on one particular gene within one type of
> segmental duplication originating from Chromsome 16:
>
> "Rapid evolution of primate genes has also
> been documented for interspersed segmental
> duplications. A 20-kb segment of chromosome
> 16, termed LCR16a, recently (12?
> Mya) proliferated, creating 15?30 copies that
> are dispersed throughout 15 Mb of the short
> arm of human and chimpanzee chromosome
> 16."
>
> One gene seemed to be replicated within this example, throughout one
> particular instance of this seg dup copies....
>
> A novel hominoid gene family (termed
> morpheus, after the Greek god of dreams who
> could change into many different human
> forms) was discovered in half of the human
> duplicates. Surprisingly, the exonic regions of
> this gene family showed accelerated rates of
> mutation when compared with intronic
> regions (FIG. 5)."
And yet more "weirdness"
>
> I believe that when I saw Eichler present this data at RECOMB he noted
> morpheus as a brain-specific protein, which is interesting. Morpheus
> is clearly a hominid-specific gene and change has been positively
> selected for:
>
> "Comparison of putative protein-
> encoding exons revealed that most of
> these changes [mutations] (>95%) resulted in amino-acid
> changes. Consequently, average coding
> sequence divergence (15?20%) among copies
> between human and chimpanzee far exceeds
> the amount of intronic sequence divergence
> (1?2%)."
>
> Since the "neutral" areas of the genome -- the non-coding areas -- in
> the region of these duplications are mutating at 1-2% divergence rate
> between chimps and humans, and the protein-coding (functional) area of
> this protein is mutating at a much faster rate (20% divergence) then,
> therefore, the changes in the functional regions are *selected for*.
That's one possible explanation. But assuredly not the only one. It
makes me think that these changes are being directed, most likely by
the genome itself.
Your scenario still relies on random mutations, and asssuming that
those mutations in functional areas are occurring faster because
they're being selected. I don't think we know enough about how the
genome works to come to that bold conclusion. There might be other
mechanisms at work of which we are unaware.
>
> "Analysis of this gene family among
> hominoids shows that the main episode of
> enhanced amino-acid replacement occurred
> after the separation of human, chimpanzee
> and gorilla lineages from the orang-utans (30-
> fold accelerated rate of amino-acid replacement
> when compared with neutrally
> evolving DNA)."
>
> Not only were these genes replicated, but were also changed up through
> the primate lineage.
By random, fortuitous accidents or by some other process?
In my experience, meaning and function have never arisen from random
processes.
This is a step in the right direction.
>
> A discovery of a mechanism for gene innovation will also possibly help
> explain why primates were able to "accelerate" into a greater
> intellectual capacity.
Once again, this depends on these innovations just "springing up" by
accident. I'm not able to buy into the notion that the higher
capacities of humans, the abstract thinking, the emotions, the complex
behaviors that we display just "popped up" by accident". Take fosB for
example. It's a gene that regulates the nurturing response. In
knockout experiments, when this gene was disabled, the mothers failed
to nurture their young and they died. Where did this gene come from?
Did it accidently "evolve"?
>
> This next conclusion should not be under-estimated. The implications
> for these findings are enormous. They actually point to the mechanism
> by which primates are distinguished from other animals.
>
> "Second, the process provides the opportunity
> for the duplication and transposition of genes
> into new chromosomal environments that
> allows them to evolve unencumbered by selective
> constraint. The recent origin of segmental
> duplications provides an ample substrate for
> both the alteration of existing genes and the
> birth of new ones. It is, therefore, not implausible
> that new genes with altered functions have
> emerged that distinguish man and great apes
> both at the phenotypic and genotypic level."
Just having "new" genes arise is only a very small part of the
problem. If the duplications are of the old genes, then they perform
the old function, or if they are defective, they perform no function
at all. Genes are the set of instructions that direct processes. Any
"new" gene would possibly find itself either directing the old
process, or having a function for which no process or structure yet
exists, or being totally non-functional. The entire genome of an
organism has to work together, to be integrated into the context of
the organism. In the trnasition from chimps to humans (if such a
transition did occur), would require changes in many, many genes,
those for brain function, nervous function, bone structure,
musculature, etc. All of these fortuitous variations would have to
occur together, in context and in a meaningful way. No one has yet
demonstrated how these new genes can integrate themselves into the
overall structure and functioning of the organism. It's a daunting
task, and IMHO, well beyond the realm of chance.
In addition, these "new" genes would have to deal with a genome
that contains more information than can be accounted for by a linear
array of descrete sequences. This may seem puzzling until one
considers the ramifications of pleiotropy, embedded and overlapping
genes, control functions which are embedded within the genes
themselves, breakdown proteins which have functions unrelated to the
mother protein, etc. And it is not just the complexity of these
processes and interactions that is so challenging for us, it is the
incredible ingenuity that is manifest in their design. Nothing random
or accidental is happening in the genome. New adaptations are not
arising out of coding and other types of errors. The genome is doing
exactly what it's supposed to do with purpose and precision. We just
don't understand it.
>
> So...
> Eichler showed that some of these primate-specific areas show the
> development of NEW GENES that exist nowhere else in the animal
> kingdom.
>
> There is evidence for positive selection WITHIN the genes in these
> recent duplications.
>
> The mechanisms that Eichler examines are ways for genotypes to
> innovate new genes, but I've yet to see how a mechanism such as
> segmental duplication contradicts Darwinism in any way. It in fact
> supports it, since until Eichler took the time to examine the "genetic
> fossils" within our DNA, mechanisms for innovating new genes were
> unclear in the primates, at least.
But the reson why this occurs is still a mystery. Like I said before,,
we've only taken the very first baby steps. A whole universe of
transcendant beauty and complexity is waiting to be discovered. There
is nothing random and nothing accidental about what we're seeing. We
are like Leewenhoek in the 17th century, peering through his primitive
glass and seeing cells. The vast complexity and purposefulness of the
cellular functions were invisible to him, and so he believed that a
cell had only three simple parts. And so we are today, some of us
still believeing that this vast complexity that we see before us, this
thing called life, is the result of a process so trivial as to be
unworthy of mention, let alone granted the power to create a structure
as complex and beautiful as the human mind.
>
> Segmental duplicaiton shuffling and redistribution of genetic material
> within chromosomes is a mechanism for generating new genetic material,
> itself. Within the this does not somehow question the /result/ of
> these mechanisms, which is diversification of genotypes which can
> respond to evolutionary pressure in a more plastic and adaptable way.
>
> > Those who insist on
> > clinging to the old paradigm and who continue to try to shoehorn these
> > new discoveries into the old molds will be left behind.
>
> I don't understand why you think this needs to be "shoehorned" in. Can
> you be more specific, as to exactly WHY these results go against
> evidence for selection? Because the results found evidence for
> selection. You don't need to shoehorn the conformation of selection
> events into Darwinism.
Selection can change the frequency of already existing alleles in a
population under selection pressure. It has no creative power beyond
that. And it can only select what's there to be selected. So you've
got to explain where the genes came from. Not just the genes, but the
meaning they convey, the context in which they function and the
interrelatedness of all of them working together. These investigators
and others *expect* selection to be a factor, and so when asked to
provide an explanation for what they see, they fall back on this
mechanism, sometimes ignoring the fact that there might be many other,
equally believable explanations. Try to wipe your mind completely
clean of any darwinian biases (an impossible task, I'm sure) and then
look at these data again. You just might see something different.
>
> > But it's a
> > little like what we heard in the 60's about civil rights. The people
> > said that "these things take time, we can't change decades of behavior
> > in one day. Be patient" And so it is in science. You can't change
> > deeply ingrained thought patterns over night and you have to expect a
> > lot of resistance from the "statics" who insist on clinging to past
> > dogma.
>
> I think what I've been saying all along is falling on deaf ears, here.
> I hope not.
You have no hope of convincing me that darwinism is the mechanism of
evolution any more than you could convince me that there really is a
Santa Claus who comes down the chimney on Christmas Eve. Once you grow
beyond these kinds of myths, there really is no going back. What I am
hoping is that you will listen to what I'm saying, and something that
I might offer will light a spark, or make you think about the problem
a little bit differently. This may sound arrogant, but I hope not. I
don't mean to be condescending and I have the greatest respect for all
scientists and the work that they do, but it's so frustrating to see
so many people mired in an obsolete and outdated paradigm that should
have been discarded long, long ago.
>
> I'm telling you that dogma does not get one the Nobel prize.
Who wants a Nobel prize? Not me, that's for sure.
As Feynman aptly put it:
"I don't like honors. I'm appreciated for the work that I did, and
for people who appreciate it, and I notice that other physicists use
my work. I don't need anything else. I don't think there's any sense
to anything else. I don't see that it makes any point that someone in
the Swedish Academy decides that this work is noble enough to receive
a prize. I've already got the prize. The prize is the pleasure of
finding the thing out, the kick in the discovery, the observation that
other people use it. Those are the real things."
>
> Scientists are chipping away at foundations all the time. Sometimes
> all they reveal is new, stronger foundation.
No one that I can see is "chipping away" at darwinism. In fact people
like Dawkins and Dennett are extending it even further. It's now moved
out of the realm of science, I believe. The same rules that apply to
all other sciences don't seem to apply. My personal opinion, and I'm
not going to name any names or anything like that, but my personal
opinion is that if I was a young research scientist in 2002, just
starting my career, looking for a post-doc slot, or a tenure-track
job, depending on funding and getting papers published, I would not
oppose darwinian evolution simply out of a strong sense of
self-preservation. Even well known people, whose names you would
immediately recognize, are afraid to say too much lest they become
pariahs and outcasts. It's not hard to see how science punishes
heretics. The history of science is full of literal and metaphorical
"burnings at the stake".
>
> If you think that all young scientists and students have a century's
> worth of work beat into their heads when they emerge into their
> professional careers...to make them some kind of robot automaton, then
> CLEARLY you don't know most scientific graduate students, or you have
> a ridiculous idea of what real-life people are like.
I know what real-life people are like. In the words of H.L. Mencken,
(paraphrased) "people will renounce any principle, no matter how
precious to them, and adopt any lunacy, however offensive to them, in
order to keep their place at the trough".
>
> Evolution is accepted as a consensus of data. It's not a mantra that
> is beat into the heads of young scientists. Evolution was mentioned as
> a PASSING THING to me as I was studying chemistry, physics, and
> molecular biology. "Oh, by the way, the data appears to be best fit by
> the evolutionary theory we have today." I don't call that dogma.
Well, I imagine that a lot of young scientists have a bit of tunnel
vision about their own area of expertise and may not take the time to
investigate all of the facts relating to other areas of science. When
told by others that this is the consensus, they accept that. Those who
go into evolutionary biology are those with a vocation, or a calling,
like for the priesthood. It's hard if everyone else is saying one
thing, for a single person to say anything different. It takes a lot
of courage. Someone like me who doesn't get his living from the
science establishment, is free to speak his mind. But often to great
ridicule and disdain. That's why I love people like Lynn Margulis,
Barbara McClintock and others like them who know the truth and are not
afraid to speak it.
>
> If you came up with data that goes against evolutionary theory, and
> was repeatable, you'd become famous and there would be a scramble to
> try to figure it out. If you come up with data that extends
> evolutionary theory, then yea, you're going to get people saying it
> extends evolutionary theory. Your complaint earlier, that people just
> are able to fit new data easily into evolutionary theory by positing
> "made up scenarios" to fit the data begs the question...why are they
> so easily able to do that? Sure, evolution should be able to be
> falsifyable. It can be falsifyable in a number of various different
> ways. Find an animal who survives in an environment who is not native
> to that environment.
> Humans are the exception because we can engineer our environments to
> suit us.
Darwinism is probably not falsifiable because it's almost impossible
to prove that something didn't happen the way someone says it does.
Added to that is the fact that the theory, as you described yourself,
is basically whatever the individual says it is. The response is
always "you don't understand evolutionary theory, it doesn't say that
at all" If you attempt to define it before attacking it, you'll be
accused of putting up a "strawman" argument. No, the evolutionists
have an answer for everything. And they're pretty good at it, since
they've been defending this theory for over 100 years. But the
creationists have called them out, and now the hoax is being exposed.
But organized science still has a great deal of political power and
will use it when needed. It's a classic battle and it's been going on
for thousands of years. The definitive example is when the gaps in the
fossil record were exposed. "Punctuated equilibrium" was the new, best
story. But that backfired because it only drew more attention to the
problem instead of dousing the flames.
Right. The frequency of already existing alleles in a population can
change as a result of selection pressure. If that's all you mean by
'evolution" and "darwinism" then fine. But how do you explain the
origin of the eye, and the Krebs cycle, and protein synthesis and
blood clotting, and....on and on?
>
> The mechanisms for ESTABLISHING those genotypes which are THEN
> selected for are what you and I have been talking about, here. Those
> are mechanisms FOR natural selection. Those are mechanisms which allow
> natural selection to occur with some "winners" at the end. You
> haven't shown me how any of these mechanisms go against Darwinian
> evolution.
You've failed to show how natural selection can create new
adaptations, processes and structures. All I see are changes in gene
frequency in populations.
>
> > No evidence of any kind has
> > yet been presented that these kinds of changes in the genome, from
> > simple point mutations to complex restructuring of large segments of
> > the genome can ever lead to new major adaptations, processes,
> > functions, structures or organisms.
>
> Maybe I should start bringing up HOX function, now. Want to talk about
> how point mutations in HOX regions affects the timing of embryonic
> development and actually makes morphological change apparent?
I read the paper. Don't have the cite handy.
> Speciation is also suggested in Eichler's work. But I skipped most of
> that.
>
> > The evolution that we see is
> > trivial, and only involves minor changes. We still seem to cling to
> > the notion that these trivial changes can somehow lead to the creation
> > of complex new adapatations. We imagine that the impossible can be
> > made possible, if we just cut it up into small enough steps and give
> > it a sufficient amount of time.
>
> We don't cling to any such idea. We have evidence for these processes.
> Care to tell me how everything you've just quoted is not evidence for
> what you're arguing against?
You've failed to demonstrate a nexus bewteen selection and major
adaptive changes. All the evidence says that "genes and chromosomes
change" We know that. "Mutations occur". We know that. "Selection
occurs" We know that. Now show that these effects can somehow lead to
new structures and processes and adaptations. Bridge the gap, don't
rely on just a "leap of faith".
>
> I don't call restructuring of a genome "small scale", nor do I call
> the change from ape to human "small scale" at least from this end.
>
> > > > So, when you say that "evolutionary theory is challenged every day
> > > > by scientists doing experiments" it makes me wonder what you mean by
> > > > "evolutionary theory" and also, what these experiments are that you're
> > > > referring to. I have never seen any evidence of any experiments that
> > > > have supported the idea that mutation and natural selection is a
> > > > mechanism that has anywhere near the creative power vested in it by
> > > > Darwin and his successors.
> > >
> > > Have you been following the scientific literature in the last few
> > > years (not to mention the last 20 years)?
> >
> > Yes, and it tells me that darwinism is dead but they just don't know
> > how to break the news to us.
>
> You're kidding, right? Who is "THEY"? Honestly, Charlie, who is
> "They"? There is no "they". That's purely paranoid.
<Humor>
Yes, and it tells me that darwinism is dead but they just don't know
how to break the news to us. :-)
</Humor>
Better?
>
>
>
> > <SNIP cites>
> >
> >
> > >
> > > > Perhaps you could also clarify what you mean by "evolutionary
> > > > theory". It has many faces and many aspects. Do you mean "species
> > > > change over time", or do you mean "changes in the frequencies of
> > > > alleles in a population", or do you mean "neo-darwinism" or
> > > > "ultradarwinism" (Dawkins, et.al.) or do you mean "neutral theory" or
> > > > something else?
> > >
> > > I mean evolutionary theory as it stands in general consenus today,
> > > beginning with natural selection, species change over time (both
> > > gradual and punc/eek), and molecular basis for evolution that is
> > > sometimes referred to as various different labels, depending on whom
> > > you ask. I really could say that all of these various brands of
> > > evolutionary theory are being tested by various people all the time.
> > > Go to PubMed and type in "evolution". You'll get over 50,000
> > > references. Some of them are certainly spurious, but a solid
> > > proportion of them will address biological evolution. I say this in
> > > order to make the point that there are many people from various
> > > backgrounds interested in the subject.
> >
> > There is no general consensus that I can see. It seems to me that
> > "evolutionary theory" is whatever the person you're asking says it is
> > and as you point out "all the various brands of evolutionary theory
> > are being tested..." So the word "evolution" has no particular
> > meaning at all. And there is no one particular "evolutionary theory".
>
> You're right.
How seldom I hear that. Let me savor the moment ;-)
By the strictest standard, there IS NO ONE EVOLUTIONARY
> THEORY IN THE DETAILS. There is only the theory which BEST FITS THE
> DATA and in the outlier details it's still hazy because there isn't
> enough detail in the data yet to fill in the gaps.
So it's unfalsifiable. There is a very important characteristic of a
scientific theory or hypothesis which differentiates it from, for
example, an act of
faith: a theory must be falsifiable. This means that there must be
some experiment or possible discovery that could prove the theory
untrue. If there is no one evolutionary theory, and it changes every
time someone adds something new, then it is not a scientific theory.
Darwin's original theory stated that evolution occurs through the
gradual accumulation of fortuitous and beneficial variations over a
long period of time. When it was demonstrated in the fossil record
that there was no evidence for this, the theory simply mutated into
something else. This is not science as I know it.
>
> > I try to not make that same mistake. I don't attack "evolution"
> > because nobody knows what it means. I attack "darwinism", which is
> > still a little murky, but not as bad as "evolution"
>
> Darwinism suggests speciation through selection and divergence. Again,
> I don't see how anything we've talked about here denies that.
>
> >At least with
> > darwinism, most people know you mean something about variation and
> > selection. But even that is murky, because Darwin was firmly against
> > "leaps" and insisted that his mechanism relied on the gradual
> > accumulation of fortuitous variations over a very long period of time.
>
> Darwin was also operating in 1850 before anyone knew anything about
> genetics. But we know that.
So, would you then say that Darwin's theory of Natural Selection, as
set down in 1859, has been falsified and is no longer considered to be
correct?
Had to look that one up. Pedantic.
But I hope you would agree that we still don't know the etiology of
these "new" genes, and whether they are the result of random,
accidental processes or directed processes, either from within the
genome or from without.
Dick C
news:abshaq$5el$1...@helle.btinternet.com:
>
> "Derek Stevenson" <derekste...@yahoo.com> wrote in message
> news:abr1dn$khnr0$1...@ID-139629.news.dfncis.de...
>>> In science, unlike in law, the verdict is automatically subject to
>> appeal whenever new evidence becomes available. And in science, again
>> unlike in law, anyone with the proper facilities is free to conduct a
>> fresh trial of the accused and come to a verdict of their own.
>>
>> So now, it's not the same lack of reasonable doubt -- it's actually a
>> far higher standard.
>>
>
> LOL, the same higher standards that gave us thalidomide no doubt, plus
> numerous other scientific disasters.
Ah yes, thalidomide. A disaster only because it was prescribed for
pregnant women. Of course, in the 50's all sorts of things were
prescribed for pregnant women. Not the fault of science, rather the
fault of doctors. Thalidomide is to this day, one of the best drugs
on the market for males and women who are not going to give birth.
It is also being shown useful in the treatment of leprosy and was,
at least for a while, being researched in the treatment of aids.
> By the way I agree that these are the highest standards that may be
> possible, ,( human greed and lust for fame being the exceptions,) as
> they deal with human life, ,, death and deformity are the
> alternatives. Unfortunately they don't even begin to apply where
> evolutionary science is concerned.
Unfortunately, you do not know what you are talking about. Science
has high standards, and the standards apply in biology as well. What
you see are the anti science folks trying to drag various parts of
science down to their level. They do that with lies and mud slinging.
> So basically don't expect any standards at all, no one is going to
> live or die because of evolutionary beliefs, and there arn't going to
> be any inquests with relatives and the general public screaming for
> blood and facts.
Evolutionary theory has applied to medicine. And because of knowledge
of evolution we understand why bacteria are immune to antibiotics,
and why new strains of disease crop up, and we are learning how
to deal with them. Your assertion about living and dieing is just
as false as the rest of your post.
> Which as history has shown is just about the only way you'll ever get
> anywhere near the real truth for anything.
Actually, that is not what history shows. Getting to the truth
depends upon evidence, not on how many people complain. But if enough
people complain about how creationists are destroying our science
education perhaps things will improve.
--
Dick #1349
"Believe those who are seeking the truth; doubt those who find it."
Andre Gide, French author and critic (1869-1951).
email: crav...@msn.net
Lilith
Eichler's work can't be clearer on that subject (previous post).
>In fact we can't say anything at all about the origin of
> the genes. They could just have well come to the earth from elsewhere
> already containing the information that they use or they just as well
> may have been generated by other genomes by some sort of unfolding of
> an algorithm that was already present.
Not being able to say where genes come from is not evidence against
selection. It's lack of evidence as to the origin of genes.
> Evolutionists are seeing
> "relatedness" and they are automatically assuming an evolutionary
> explanation.
We've seen genes appear that weren't there in ancestral states. See
previous post.
> And this may well be because they are working from the
> premise that "evolutionary theory" is correct and therefore they may
> be explaining everything they see in the light of that pre-existing
> bias, rather than as new data.
That might be true if it was one experiment with one set of data. The
interesting thing is that you can assume a different subset of
assupmtions in every experiment and get confirmation of your
experiment. Add up enough of these and you get overlap. I don't see
what the problem is, here. I haven't seen any huge gaps in a consensus
evolutionary theory that can't be eventually filled in by more data as
it comes available. Selection is apparent. Genetic drift is apparent.
Etc.
>The fact is, IMHO, the fact that all
I still don't see how an argument from incredulity can make any kind
of case when there's no rates, no data, no known conditions, no facts
to be incredulous against. There's no data on the ability or inability
of any of these molecules springing forth from any kind of primordial
soup. There's incredulity in both directions. In otherwords, it's
null. So to say that an argument from incredulity is a strong argument
against earthly development is selectively ignoring the other half of
the argument, in that there's equal problems with assuming that it's
not of earthly origins, and in some people's opinion, much less
possible.
> >
> > >On a macro
> > > level, there are countless questionable observations that dispute
> > > darwinism. The gaps between classes that shouldn't be there.
> >
> > Such as? Give me some specifics, here.
>
>
> Well, I don't want to get into a whole thing about transitional forms,
> that's a bottomless pit if ever there was one. Suffice it to say that
> the fossil record tells us almost nothing about the evolutionary
> origin of phyla and classes. Intermediate forms are non-existent,
> undiscovered or not recognized. Ask any paleontologist.
There are whole papers and research on transitional fossils. Which
paleontologist says there's none?
> >
> > > The
> > > sudden appearance of all of the known animal phyla in a very short
> > > time and the appearance of no new phyla over the next 500 million
> > > years.
> >
> > Someone could remind you here that the fossil record is necessarily
> > incomplete. But I don't have to do that, do I?
>
> After 142 years of looking by plenty of grad students and post-docs,
> one would expect that at least one example of *most* extinct forms
> would have been found. A large percentage for sure. There are god
> knows how many millions of living forms, I don't know the number
> exactly, we have far fewer extinct forms represented than extant
> forms. It ought to be the other way around, shouldn't it?
That's a straw man argument. You know as well as I do, if you have any
kind of scientific background, that fossils only form under specific,
specialized conditions, usually having to do with sedementary
deposits. If you die outside of a body of water or some kind of
special dessicating/preserving environment, your remains won't be
found. That's why we make such a big deal out of mummies, for
instance.
> >
> > >The fact that the fossils of the Burgess Shale and the fossils
> > > of the Chengjiang region show no significant differences despite the
> > > fact that they are separated in time by 40 million years, in a time
> > > when evolution was allegedly proceeding at a very rapid rate.
> >
> > Define "no significant difference", and I'd like some scientific
> > references, please.
>
> "Fossilized Soft-bodied Fauna", Chen Jun-Yuan, Jan Bergstrom and Hou
> Xiangguang
> National Geographic Research and Exploration, Winter 1991
>
> An exerpt from his conclusion:
>
> "In fact, evolutionarily, the Chengjiang arthropods
> are not much different from those of the Burgess Shale, despite their
> distinctly older age, and, hence, do not bring us much closer to the
> origin
> of arthropods, at least not from a morphological point of view.
> Part of the importance of the Chengjiang fauna mav lie in the
> implication
> that the initial coelomate radiation was extremely rapid and
> morphologically far-reaching. The Middle Cambrian Burgess Shale fauna
> shows several of the animal phyla we meet in the seas today.
> A step back in time some tens of millions of years brings us to the
> Early
> Cambrian Chengjiang fauna. During this time span, evolution seems to
> have produced very little change."
How does this go against evolution? There have been species who have
seen very little change over the eons. Some have appeared quite
suddenly. If you have a rich niche that doesn't require a lot of
evolutionary pressure to adapt to, then why would a species adapt?
>
>
> >
> > > Anyone who takes the time to think about this with an open mind
> > > and just looks casually at the actual evidence cannot help but discard
> > > this theory immediately. I don't believe in darwinism for the same
> > > reason that I don't believe in the tooth fairy. Or god.
> >
> > I beleive in darwinism because I play with its consequences every day.
> > I suppose I could have an "open mind" and be ready to accept any other
> > theory that comes along, but Darwinism is how I, and the company I do
> > research for, gets results (see above methods for a small smattering).
>
> Darwinism is a mechanism, based on variation and selection. There is
> no question that mutations occur and there is no question that
> selection can change the frequencies of alleles in populations. What
> is lacking is evidence that these trivial effects can produce major
> adaptive changes, new structures and processes and new organisms. With
> all due respect, and feel free to correct me if I'm wrong, it would
> appear to me that this question regarding the creative power of
> darwinism is not something that enters into your daily activities.
I view genetic diversity and development as major changes. I'll reply
more on this later as I have a 10am meeting and it's getting late. :)
>
> >
> >
> > >
> > > >
Lilith
> Seconded. Lilith : you won't convince Mr Wagner : he's unconvincable.
> However I just want you to know that your post found (at least) one
> fascinated reader - you must have a very interesting job.
>
> Gavin
Thanks, Gavin. I like my job a lot. It's officially titled
"bioinformatics" but I get to play with a whole toolbox of things. I
think I should post a faq on how to delve into genomes for the
interested, it's not that difficult.
Lilith
> cha...@charliewagner.com (charlie wagner) wrote in message news:<ec838d5.02051...@posting.google.com>...
> > lil...@umich.edu (Lilith) wrote in message news:<75200cbc.02051...@posting.google.com>...
> > > I beleive in darwinism because I play with its consequences every day.
> > > I suppose I could have an "open mind" and be ready to accept any other
> > > theory that comes along, but Darwinism is how I, and the company I do
> > > research for, gets results (see above methods for a small smattering).
> >
> > Darwinism is a mechanism, based on variation and selection. There is
> > no question that mutations occur and there is no question that
> > selection can change the frequencies of alleles in populations. What
> > is lacking is evidence that these trivial effects can produce major
> > adaptive changes, new structures and processes and new organisms.
Someone else in another thread pointed out Francis Ayala's work on
fruit flies leading to speciation. There is other "smoking gun
evidence" which is pretty compelling. It lies in the examination of
the reproductive proteins through several species.
Here's another bit of recent research on the rapid evolution of
reproductive proteins.
Conjecture time. I believe selection at the reproductive protein level
gives rise to what I call "speciation pressure"...if a sub-population
does not recombine with the larger population as quickly as the
changes in the male/female sex-specific genetic complement evolve,
male/female co-adaptation and rapid evolution of reproductive proteins
will force them into another species.
There can be no other direct (genetic/molecular) reason for speciation
except that the reproductive compliment of one species no longer
interacts with the reproductive compliment of another. This acts as
the absolute seperation event to genetic recombination.
The reproductive apparatus will not work if divergent animals in a new
species try to mate with animals in the same species. Let me dig into
the following review to clarify.
( All quotes and data from Swanson W. and Vacquier V. "The Rapid
Evolution of Reproductive Proteins" Nature Rev Gen. (3) Feb 2002 p
137-144)
First, some data to consider before I go on.
Rapidly evolving reproductive proteins between Mouse and Human
-------------------------------------------------
FIGURE 1: Rapidly evolving reproductive proteins (those that fall
among the general population of the most 10% most divergent proteins
between mouse and human)
Rank Protein Divergence in percent.
1 Transition protein 2 68
48 ZP2 43
59 Protamine P15 41
86 Sperm protein 10 39
92 Testis histone H1 38
101 Acrosin 38
120 Protamine 2 36
161 ZP3 33
194 Testes Tpx1 31
Figure 1 Rapidly evolving proteins. Comparison of 1,880 human/rodent
orthologues from Makalowski & Boguski plotted as a frequency of the
occurrence of genes with a varying percentage of amino-acid
divergence. The portion that contains the 10% most divergent proteins
is shown in blue; reproductive proteins that are among the 10% most
divergent proteins are listed. Tpx1, testis-specific protein 1; ZP2/3,
zona pellucida 2/3.
----------------------------------------------------
And, TABLE 1:
Table 1 | Rapidly evolving genes involved in fertilization
Gene Function Organism Reference #
(see end of post)
Pheromones Mating and cell growth Euplotes 12
(such as Er1) (ciliate, protozoa)
mid1 Determines mating type Chlamydomonas 13
+ or - (green alga)
fus1 Mediates cell fusion Chlamydomonas 14
Sig1 Involved in cell mating Thalassiosira 15
(diatoms)
Pheromones Mating-type pheromone Basidiomycetes 17
(such as Phb.3.2) (fungi)
SCR Sporophytic Brassicaceae 18,19
self-incompatibility
S-locus Gametophytic Solanaceae 22
self-incompatibility
Lysin Dissolves egg envelope Tegula and abalone 24,26
(Mollusca)
sp18 Fusagenic sperm protein Abalone 28
TMAP Major acrosomal protein Tegula 29
Bindin Adheres sperm to egg Sea urchin 34,35
Acp26Aa, Sperm usage and Drosophila 49,51,52
Acp36DE storage
Ph-20, Sperm-surface Mammals 54
b-fertilin recognition
ZP3 Egg inducer of sperm Mammals 10
acrosome reaction
ZP2 Egg envelope, sperm Mammals 10
binding
OGP Oviductal glycoprotein Mammals 10
Zonadhesin Sperm surface Mammals 59
TCTE1 Mammalian Mammals 60
spermatogenesis
------
(Acp, accessory-gland proteins; Er1, E. raikovi pheromone type 1; OGP,
oviductal glycoprotein; SCR, S-locus cysteine-rich; TCTE1,
t-complex-associated-testis-expressed 1;TMAP, the major acrosomal
protein; ZP2/3, zona pellucida 2/3.)
========================================================
Swanson and Vacquier comment on the study by Makalowski and Boguski
(what names!):
"Rapidly evolving genes are those that encode proteins with a higher
than average percentage ofamino-acid substitutions between species.In
one study,Makalowski and Boguski compared 1,880 proteins that are
encoded by ORTHOLOGOUS GENES from humans and rodents,which represent
~5% of all predicted human genes. Fifty per cent of them showed less
than 10% divergence at the amino-acid level (FIG. 1),and 209 fell
within the range of 30-70% divergence."
This is within my experience. It's very helpful that mice seem to have
about 60-80% similarity on average in genes and gene structure (but
not chromosome location...that's often different!) That's what makes
them good (but not perfect) models for molecular biology study.
"Although many of these most rapidly evolving genes are involved in
the immune response, eight are involved in reproduction.Three of them
- ZP2 (zona pellucida glycoprotein 2), ZP3 and ACR (acrosin) - are
directly involved in the sperm?egg interaction."
I might also mention that sperm/egg binding is sensitive to species. I
wish I could just quote the entire article, but that's against
copyright. So I'll mention just a few examples in a bit...
"The sperm-egg interaction that leads to gamete fusion and zygote
formation is most efficient if the sperm and the egg are from the same
species. Even in very closely related species ofsea
urchins(33),fruitflies(61),nematodes(62) and mammals(63),strong
barriers to cross-species fertilization have evolved.The phenomenon of
species-specific fertilization shows that the proteins that are
involved in gamete recognition must have a species-specific structure
and that they must bind each other with species-specific affinity."
There has been work with sea urchins, Drosophila, abalone, and other
organisms to show that it's often not as simple as "sperm binds to
egg". For example, there are several factors ('accessory gland
proteins') that the male Drosophila includes with his sperm when
mating with the female, including sperm competition factors (this
isn't surprising, is it?). When one species of Drosophila, D. suzukii
are crossed with D. pulchrella, they do not produce hybrid offspring
UNLESS the D. suzukii females are provided with injections of
accessory-gland extracts from D. pulchrella males. The
species-specific accessory gland proteins are required for
reproduction.
"So,a pair or a suite of fertilization proteins - that is, one or more
male and female proteins - has to co-evolve to maintain their
interaction.The inability of sperm to fertilize eggs creates a
reproductive barrier that could subdivide populations into species.But
how does species-specific fertilization evolve? And when does this
evolution occur? does it happen at the early stages of species
divergence,or do the changes accumulate only after speciation?"
Conjecture time. Can two populations, seperated by either sexual
selection criteria (a different song, a brighter plumage, a different
scent, a different courtship ritual based on a changing food supply
availabilily, etc) or another force, such as geography or environment
seperate out two populations so that when they re-converge their
reproductive proteins have out-evolved one another? Another
consideration the authors don't mention is what happens if an
environmental niche changes morphology, and sexual selection can't
keep up with morphological change through an entire population? What
if some females or males start choosing mates based on individual
trends in "preference" while this adaptation is going on, so some
traits get more rapidly fixed than others, while in some
sub-populations, other traits get fixed? But we know we women are
picky. ;)
" The fact that proteins that are involved in such a crucial
process as fertilization are not conserved poses an interesting
question for evolutionary biologists: Why are reproductive genes
evolving so rapidly,and what is the functional consequence of this
rapid evolution?
To find answers to some of these questions,evolutionary
biologists have turned to one of the most extensively characterized
animal fertilization systems,that of the abalone,because amino-acid
sequences for lysin and its receptor, VERL, are known for several
closely related species of the abalone."
See for example
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=VERL+abalone
The lysin molecules actually adhere to the abalone egg's VERL
receptors and the VERL receptors then act as a kind of pliers to
spread-apart the egg's vitelline envelope and allow the sperm entry.
This is a very abalone-species-specific reaction, in that sperm from
one species of abalone cannot perform this task on eggs of another
species of abalone.
"Amino-acid sequences of lysins from different abalone species are
remarkably divergent and are excellent examples of adaptive evolution
25,26.The cause of rapid evolution of lysin might lie in the structure
of VERL;it is a large,~1,000 kDa glycoprotein that contains 22 tandem
repeats of~153 amino acids.In contrast to lysin,VERL shows no evidence
of positive Darwinian selection;instead,it seems to be evolving
neutrally.The 22 tandem VERL repeats are subject to concerted
evolution ? the mechanism by which ribosomal genes evolve 30,66, in
which unequal crossing over and GENE CONVERSION randomly homogenize
the sequence of tandem repeats within the gene and within a population
66,67."
The end result is that the repeats in the VERL receptor from one
abalone species are more similar to one another (inside the one
species) than they are to other VERL in other species. This supports
the model the authors continue on to discuss, in which small neutral
changes in VERL forces the choice of an appropriately modified lysin
in an animal who has the mutation. The authors note that in a sea and
current-borne population, this kind of speciation is completely
possible based on the ability of populations to become isolated.
For fun, I've aligned a handful of VERL sequences from two abalone
species for everyone and put it up on a webpage.
http://www-personal.umich.edu/~lilyth/abalone_VERL.htm
(Alignment of VERL (vitelline envelope receptor for sperm lysin)
For Haliotis corrugata and Haliotis rufescens, two species of
abalone.)
Note that there are changes to VERL both WITHIN a species as well as
OUTSIDE a species, and the changes appear small (one or more amino
acid differences) but it's a big enough difference to prevent
corrugata from inseminating rufescens.
"What drives reproductive protein evolution?
Although distinct evolutionary forces might act in different
organisms,the rapid evolution of reproductive proteins seems to occur
in several diverse taxonomic groups (TABLE 1).We propose that the
selective forces of sperm competition,sexual selection and sexual
conflict, could individually,or in combination,provide the selective
force that drives the rapid evolution ofreproductive proteins.Sperm
competition83(also referred to as sperm precedence84) occurs because
each sperm competes with all the other sperm to be the first to fuse
with the egg."
In sea urchins alone there are 200 billion sperm cells per five
milliliters of water! One of the arguments against mutational
selection is that there aren't enough population to generate the major
kinds of changes we see in animals today. However, that is 200 billion
genetic experiments in one 5ml cube of water, each of which can be
selected for based on a molecular determination of fitness (egg
receptivity). It's not only organisms which can be selected for, it is
also reproductive cells, and their reproductive proteins.
"Sexual selection at this [sperm-egg] cellular level is known as
cryptic female choice (85),and it might come into play when an egg
prefers to bind to a sperm that carries a particular allele of a
sperm-surface protein,whereas another egg has little affinity for that
same sperm type. The preference of Echinometra eggs to be fertilized
by sperm that carry the same bindin allele as they do is a good
example (75)."
The authors also go on to speak about sexual conflict, when there are
many sperm available from different males. Sperm competition is a
problem for the ovum, because it has to be able to select ONE sperm or
else not reproducing at all. The first sperm to interact with the ova
of many species, including sea urchins, frogs, worms, abalone...set
off a rapid change in the electronic potential of the egg's membrane,
which prevents fusion with any other sperm. Eggs that are capable of
setting up selective blocks against polyspermy (multiple
fertilizations) are expected to be more successful and able to
reproduce. However, mammalian ova do not have this kind of reversal in
the electronic potential at their disposal. There have to be other
mechanisms (still being studied, but suspected to be the zona
pellucida egg coat proteins (ZPs)). The ZPs show evidence of adaptive
evolution, which raises the important point that sperm-egg protein
interactions must evolve in step with one another, so that certain ova
are more predisposed to certain sperm.
But what's the point of all this? The authors say
"Computer models show that sexual conflict can rapidly lead to
speciation by driving the continual evolution of traits that are
responsible for reproductive isolation,such as gamete-recognition
proteins (81). Sexual conflict results in the evolution of female
reproductive traits to reduce the cost of mating,which might lead to
the coevolution of exaggerated male reproductive traits,such as
elaborate male coloration 90.So,both empirical and theoretical studies
indicate that the rapid evolution of reproductive proteins could be a
driving force in speciation (91?93)."
Online links
DATABASES
The following terms in this article are linked online to:
LocusLink:
http://www.ncbi.nlm.nih.gov/LocusLink/Acp26Aa | Acp29AB | Acp36DE |
ACR | b-fertilin | Ph-20 | TCTE1 | zonadhesin | ZP1 | ZP2 | ZP3 |
FURTHER INFORMATION
Encyclopedia of Life Sciences:
http://www.els.net/Speciation: allopatric | Speciation: sympatric and
parapatric
Access to this interactive links box is free online.
----------------------------------------------
REFERENCES
1. Singh, R. S. & Kulathinal, R. J. Sex gene pool evolution and 8
speciation: a new paradigm. Genes Genet. Syst. 75, 119?130 (2000).
2. Vacquier, V. D. Evolution of gamete recognition proteins. 9
Science 281, 1995?1998 (1998).
3. Civetta, A. & Singh, R. S. High divergence of reproductive tract
proteins and their association with postzygotic reproductive isolation
in Drosophila melanogaster and
Drosophila virilis group species. J. Mol. Evol. 41, 1085?1095 (1995).
An important paper showing that, on average, Drosophila reproductive
proteins are about twice as diverse as non-reproductive proteins.
4. Yang, Z. & Bielawski, J. P. Statistical methods for detecting
molecular adaptation. Trends Ecol. Evol. 15, 496?503 (2000).
An excellent review on the use of the
dN/dS ratio to
detect adaptive evolution (positive Darwinian selection).
5. Makalowski, W. & Boguski, M. S. Evolutionary parameters of the
transcribed mammalian genome: an analysis of 2,820 orthologous rodent
and human sequences. Proc. Natl Acad. Sci. USA 95, 9407?9412 (1998).
The authors compare many genes between rodents and humans, and provide
a good database for the comparison of rapidly, and non-rapidly,
evolving genes.
6. Li, W.-H. Molecular Evolution (Sinauer Associates, Sunderland,
Massachusetts, 1997).
7. Lee, Y. H., Ota, T. & Vacquier, V. D. Positive selection is a
general phenomenon in the evolution of abalone sperm lysin.
Mol. Biol. Evol. 12, 231?238 (1995).
8. Hughes, A. L. & Nei, M. Pattern of nucleotide substitution at major
histocompatibility complex class I loci reveals overdominant
selection. Nature 335, 167?170 (1988).
9. Yang, Z., Nielsen, R., Goldman, N. & Pedersen, A. M.
Codon-substitution models for heterogeneous selection pressure at
amino acid sites. Genetics 155, 431?449 (2000).
10. Swanson, W. J., Yang, Z., Wolfner, M. F. & Aquadro, C. F.
Positive Darwinian selection drives the evolution of several female
reproductive proteins in mammals. Proc. Natl Acad. Sci. USA 98,
2509?2514 (2001).
This is the first demonstration of female reproductive proteins being
subject to positive Darwinian selection.
11. Swanson, W. J., Clark, A. G., Waldrip-Dail, H. M., Wolfner, M. F.
& Aquadro, C. F. Evolutionary EST analysis identifies rapidly evolving
male reproductive proteins in
Drosophila. Proc. Natl Acad. Sci. USA 98, 7375?7379 (2001). 12.
Luporini, P., Vallesi, A., Miceli, C. & Bradshaw, R. A. Chemical
signaling in ciliates. J. Eukaryot. Microbiol. 42, 208?212 (1995). 13.
Ferris, P. J., Pavlovic, C., Fabry, S. & Goodenough, U. W.
Rapid evolution of sex-related genes in Chlamydomonas.
Proc. Natl Acad. Sci. USA 94, 8634?8639 (1997). 14. Ferris, P. J.,
Woessner, J. P. & Goodenough, U. W. A sex recognition glycoprotein is
encoded by the plus mating-type gene fus1 of Chlamydomonas
reinhardtii. Mol. Biol. Cell 7, 1235?1248 (1996).
15. Armbrust, E. V. & Galindo, H. M. Rapid evolution of a sexual
reproduction gene in centric diatoms of the genus
Thalassiosira. Appl. Environ. Microbiol. 67, 3501?3513 (2001). 16.
Brown, A. J. & Casselton, L. A. Mating in mushrooms: increasing the
chances but prolonging the affair. Trends Genet. 17, 393?400 (2001).
17. Casselton, L. A. & Olesnicky, N. S. Molecular genetics of mating
recognition in basidiomycete fungi. Microbiol. Mol.
Biol. Rev. 62, 55?70 (1998).
18. Schopfer, C. R., Nasrallah, M. E. & Nasrallah, J. B. The male
determinant of self-incompatibility in Brassica. Science 286,
1697?1700 (1999).
19. Schopfer, C. R. & Nasrallah, J. B. Self-incompatibility.
Prospects for a novel putative peptide-signaling molecule. Plant
Physiol. 124, 935?940 (2000).
20. Kachroo, A., Schopfer, C. R., Nasrallah, M. E. & Nasrallah, J. B.
Allele-specific receptor?ligand interactions in Brassica
self-incompatibility. Science 293, 1824?1826 (2001).
An elegant biochemical demonstration of receptor?ligand interaction
that shows the specificity of reproductive proteins.
21. Nasrallah, J. B. Cell?cell signaling in the self-incompatibility
response. Curr. Opin. Plant Biol. 3, 368?373 (2000).
22. Richman, A. D. & Kohn, J. R. Evolutionary genetics of
self-incompatibility in the Solanaceae. Plant Mol. Biol. 42, 169?179
(2000).
23. Mayfield, J. A., Fiebig, A., Johnstone, S. E. & Preuss, D. Gene
families from the Arabidopsis thaliana pollen coat proteome.
Science 292, 2482?2485 (2001).
24. Hellberg, M. E. & Vacquier, V. D. Rapid evolution of fertilization
selectivity and lysin cDNA sequences in teguline gastropods.
Mol. Biol. Evol. 16, 839?848 (1999).
25. Metz, E. C., Robles-Sikisaka, R. & Vacquier, V. D.
Nonsynonymous substitution in abalone sperm fertilization genes
exceeds substitution in introns and mitochondrial DNA. Proc. Natl
Acad. Sci. USA 95, 10676?10681 (1998).
26. Yang, Z., Swanson, W. J. & Vacquier, V. D. Maximum-likelihood
analysis of molecular adaptation in abalone sperm lysin reveals
variable selective pressures among lineages and sites. Mol. Biol.
Evol. 17, 1446?1455 (2000).
27. Swanson, W. J. & Vacquier, V. D. Liposome fusion induced by a M(r)
18,000 protein localized to the acrosomal region of acrosome-reacted
abalone spermatozoa. Biochemistry 34, 14202?14208 (1995).
28. Swanson, W. J. & Vacquier, V. D. Extraordinary divergence and
positive Darwinian selection in a fusagenic protein coating the
acrosomal process of abalone spermatozoa. Proc. Natl Acad. Sci. USA
92, 4957?4961 (1995).
29. Hellberg, M. E., Moy, G. W. & Vacquier, V. D. Positive selection
and propeptide repeats promote rapid interspecific divergence of a
gastropod sperm protein. Mol. Biol. Evol. 17, 458?466 (2000).
30. Swanson, W. J. & Vacquier, V. D. Concerted evolution in an egg
receptor for a rapidly evolving abalone sperm protein.
Science 281, 710?712 (1998).
A model of species-specific fertilization based on molecular
evolutionary analysis of interacting male and female reproductive
proteins in plants.
31. Swanson, W. J., Aquadro, C. F. & Vacquier, V. D.
Polymorphism in abalone fertilization proteins is consistent with the
neutral evolution of the egg?s receptor for lysin (VERL) and positive
Darwinian selection of sperm lysin. Mol. Biol. Evol. 18, 376?383
(2001).
32. Vacquier, V. D., Swanson, W. J. & Hellberg, M. E. What have we
learned about sea urchin sperm bindin. Dev. Growth Differ.
37 , 1?10 (1995).
33. Palumbi, S. R. & Metz, E. C. Strong reproductive isolation between
closely related tropical sea urchins (genus
Echinometra). Mol. Biol. Evol. 8, 227?239 (1991).
34. Metz, E. C. & Palumbi, S. R. Positive selection and sequence
rearrangements generate extensive polymorphism in the gamete
recognition protein bindin. Mol. Biol. Evol. 13, 397?406 (1996).
35. Biermann, C. H. The molecular evolution of sperm bindin in six
species of sea urchins (Echinodia: Strongylocentrotidae). Mol.
Biol. Evol. 15, 1761?1771 (1998).
36. Wolfner, M. F. Tokens of love: functions and regulation of
Drosophila male accessory gland products. Insect Biochem.
Mol. Biol. 27, 179?192 (1997).
A review of Drosophila accessory-gland proteins, which have been
included in several evolutionary studies of reproductive proteins.
37. Partridge, L. & Hurst, L. D. Sex and conflict. Science 281,
2003?2008 (1998).
38. Xue, L. & Noll, M. Drosophila female sexual behavior induced by
sterile males showing copulation complementation. Proc.
Natl Acad. Sci. USA 97, 3272?3275 (2000).
39. Chen, P. S. et al. A male accessory gland peptide that regulates
reproductive behavior of female D. melanogaster.
Cell 54, 291?298 (1988).
40. Herndon, L. A. & Wolfner, M. F. A Drosophila seminal fluid
protein, Acp26Aa, stimulates egg laying in females for 1 day after
mating. Proc. Natl Acad. Sci. USA 92, 10114?10118 (1995).
41. Heifetz, Y., Lung, O., Frongillo, E. A. Jr & Wolfner, M. F. The
Drosophila seminal fluid protein Acp26Aa stimulates release of oocytes
by the ovary. Curr. Biol. 10, 99?102 (2000). 42. Kalb, J. M.,
DiBenedetto, A. J. & Wolfner, M. F. Probing the function of Drosophila
melanogaster accessory glands by directed cell ablation. Proc. Natl
Acad. Sci. USA 90, 8093?8097 (1993).
43. Bertram, M. J., Neubaum, D. M. & Wolfner, M. F. Localization of
the Drosophila male accessory gland protein Acp36DE in the mated
female suggests a role in sperm storage. Insect Biochem. Mol. Biol.
26, 971?980 (1996).
44. Neubaum, D. M. & Wolfner, M. F. Mated Drosophila melanogaster
females require a seminal fluid protein, Acp36DE, to store sperm
efficiently. Genetics 153, 845?857 (1999).
45. Tram, U. & Wolfner, M. F. Male seminal fluid proteins are
essential for sperm storage in Drosophila melanogaster.
Genetics 153, 837?844 (1999).
46. Chapman, T., Liddle, L. F., Kalb, J. M., Wolfner, M. F. &
Partridge, L. Cost of mating in Drosophila melanogaster females is
mediated by male accessory gland products.
Nature 373, 241?244 (1995).
47. Harshman, L. G. & Prout, T. Sperm displacement without sperm
transfer in Drosophila melanogaster. Evolution 48, 758?766 (1994).
48. Clark, A. G., Aguade, M., Prout, T., Harshman, L. G. & Langley, C.
H. Variation in sperm displacement and its association with accessory
gland protein loci in Drosophila melanogaster. Genetics 139, 189?201
(1995).
49. Tsaur, S. C. & Wu, C. I. Positive selection and the molecular
evolution of a gene of male reproduction, Acp26Aa of
Drosophila. Mol. Biol. Evol. 14, 544?549 (1997).
50. Tsaur, S. C., Ting, C. T. & Wu, C. I. Positive selection driving
the evolution of a gene of male reproduction, Acp26Aa, of Drosophila.
II. Divergence versus polymorphism. Mol. Biol.
Evol. 15, 1040?1046 (1998).
51. Begun, D. J., Whitley, P., Todd, B. L., Waldrip-Dail, H. M. &
Clark, A. G. Molecular population genetics of male accessory gland
proteins in Drosophila. Genetics 156, 1879?1888 (2000).
52. Aguade, M. Positive selection drives the evolution of the Acp29AB
accessory gland protein in Drosophila. Genetics 152, 543?551 (1999).
53. Fuyama, Y. Species-specificity of paragonial substances as an
isolating mechanism in Drosophila. Experientia 39, 190?192 (1983).
54. Wyckoff, G. J., Wang, W. & Wu, C. I. Rapid evolution of male
reproductive genes in the descent of man. Nature 403, 304?309 (2000).
This paper shows that rapidly evolving reproductive proteins occur in
organisms with complex mating courtships.
55. Wassarman, P. M. Mammalian fertilization: molecular aspects of
gamete adhesion, exocytosis, and fusion. Cell
96 , 175?183 (1999).
56. Yurewicz, E. C., Sacco, A. G., Gupta, S. K., Xu, N. & Gage, D. A.
Hetero-oligomerization-dependent binding of pig oocyte zona pellucida
glycoproteins ZPB and ZPC to boar sperm membrane vesicles. J. Biol.
Chem. 273, 7488?7494 (1998).
57. Chen, J., Litscher, E. S. & Wassarman, P. M. Inactivation of the
mouse sperm receptor, mZP3, by site-directed mutagenesis of individual
serine residues located at the combining site for sperm. Proc. Natl
Acad. Sci. USA 95, 6193?6197 (1998).
58. Eidne, K. A., Henery, C. C. & Aitken, R. J. Selection of peptides
targeting the human sperm surface using random peptide phage display
identify ligands homologous to ZP3.
Biol. Reprod. 63, 1396?1402 (2000).
59. Gao, Z. & Garbers, D. L. Species diversity in the structure of
zonadhesin, a sperm-specific membrane protein containing multiple cell
adhesion molecule-like domains. J. Biol. Chem.
273, 3415?3421 (1998).
60. Juneja, R., Agulnik, S. I. & Silver, L. M. Sequence divergence
within the sperm-specific polypeptide TCTE1 is correlated with
species-specific differences in sperm binding to zona-intact eggs. J.
Androl. 19, 183?188 (1998). 61. Higgie, M., Chenoweth, S. & Blows, M.
W. Natural selection and the reinforcement of mate recognition.
Science 290, 519?521 (2000).
62. Hill, K. L. & L?Hernault, S. W. Analyses of reproductive
interactions that occur after heterospecific matings within the genus
Caenorhabditis. Dev. Biol. 232, 105?114 (2001). 63. O?Rand, M. G.
Sperm?egg recognition and barriers to interspecies fertilization.
Gamete Res. 19, 315?328 (1988). 64. Swanson, W. J. & Vacquier, V. D.
The abalone egg vitelline envelope receptor for sperm lysin is a giant
multivalent molecule. Proc. Natl Acad. Sci. USA 94, 6724?6729 (1997).
65. Kresge, N., Vacquier, V. D. & Stout, C. D. Abalone lysin: the
dissolving and evolving sperm protein. Bioessays 23,
95 ?103 (2001).
66. Elder, J. F. Jr & Turner, B. J. Concerted evolution of repetitive
DNA sequences in eukaryotes. Q. Rev. Biol. 70, 297?320 (1995).
67. McAllister, B. F. & Werren, J. H. Evolution of tandemly repeated
sequences: what happens at the end of an array? J. Mol. Evol. 48,
469?481 (1999).
68. Wu, C. I. The genic view of the process of speciation. J.
Evol. Biol. 14, 851?865 (2001).
69. Rieseberg, L. H., Van, F. C. & Desrochers, A. M. Hybrid speciation
accompanied by genomic reorganization in wild sunflowers. Nature 375,
313?316 (1995).
70. Knowlton, N. Molecular genetic analyses of species boundaries in
the sea. Hydrobiologia 420, 73?90 (2000). 71. Palumbi, S. R. Marine
speciation on a small planet. Trends Ecol. Evol. 7, 114?118 (1992).
72. Hellberg, M. E., Balch, D. P. & Roy, K. Climate-driven range
expansion and morphological evolution in a marine gastropod. Science
292, 1707?1710 (2001).
73. Van Doorn, G. S. Ecological versus sexual selection models of
sympatric speciation. Selection (in the press). 74. Higashi, M.,
Takimoto, G. & Yamamura, N. Sympatric speciation by sexual selection.
Nature 402, 523?526 (1999).
75. Palumbi, S. R. All males are not created equal: fertility
differences depend on gamete recognition polymorphisms in sea urchins.
Proc. Natl Acad Sci. USA 96, 12632?12637 (1999).
This paper shows the functional consequences of diversity of
reproductive proteins, and that fertilization efficiency is dependent
on the genotype of the reproductive protein loci.
76. Biermann, C. H. & Marks, J. A. Geographic divergence of gamete
recognition systems in two species in the sea urchin genus
Strongylocentrotus. Zygote 8, S86?S87 (2000). 77. Rahman, M. A. &
Uehara, T. Experimental hybridisation between two tropical species of
sea urchins (genus Echinometra) in Okinawa. Zygote 8, S90 (2000).
78. Dieckmann, U. & Doebeli, M. On the origin of species by sympatric
speciation. Nature 400, 354?357 (1999). 79. Kondrashov, A. S. & Shpak,
M. On the origin of species by means of assortative mating. Proc. R.
Soc. Lond. B 265, 2273?2278 (1998).
80. Kondrashov, A. S. & Kondrashov, F. A. Interactions among
quantitative traits in the course of sympatric speciation.
Nature 400, 351?354 (1999).
81. Gavrilets, S. Rapid evolution of reproductive barriers driven by
sexual conflict. Nature 403, 886?889 (2000).
A mathematical model that shows how the rapid evolution of genes, such
as in those that encode reproductive proteins, can lead to speciation.
82. Wu, C. I. A stochastic simulation study on speciation by sexual
selection. Evolution 39, 66?82 (1985).
83. Clark, A. G., Begun, D. J. & Prout, T. Female ´ male interactions
in Drosophila sperm competition. Science 283, 217?220 (1999).
84. Howard, D. J. Conspecific sperm and pollen precedence and
speciation. A. Rev. Ecol. Syst. 30, 109?132 (1999). 85. Eberhard, W.
G. Female Control: Sexual Selection by Cryptic Female Choice
(Princeton Univ. Press, New Jersey, 1996).
86. Rice, W. R. & Holland, B. The enemies within: intergenomic
conflict, interlocus contest evolution (ICE), and the intraspecific
Red Queen. Behav. Ecol. Sociobiol. 41, 1?10 (1997).
87. Gould-Somero, M. & Jaffe, L. A. in Cell Fusion and Transformation
(eds Beers, R. F. & Bassett, E. G.) 27?38 (Raven, New York, 1984).
88. Stephano, J. L. in Abalones of the World (eds Shepherd, S. A.,
Tegner, M. J. & Guzman del Proo, S. A.) 518?526 (Blackwell Science,
Cambridge, Massachussetts,1992). 89. Jaffe, L. A., Sharp, A. P. &
Wolf, D. P. Absence of an electrical polyspermy block in the mouse.
Dev. Biol. 96, 317?323 (1983).
90. Gavrilets, S., Arnqvist, G. & Friberg, U. The evolution of female
mate choice by sexual conflict. Proc. R. Soc. Lond.
B 268, 531?539 (2001).
91. Barton, N. The rapid origin of reproductive isolation. Science
290, 462?463 (2000).
92. Eady, P. E. Postcopulatory, prezygotic reproductive isolation.
J. Zool. 253, 47?52 (2001).
93. Blows, M. W. Evolution of the genetic covariance between male and
female components of mate recognition: an experimental test. Proc. R.
Soc. Lond. B 266, 2169?2174 (1999).
94. Rice, W. R. Sexually antagonistic male adaptation triggered by
experimental arrest of female evolution. Nature 381, 232?234 (1996).
A description of a laboratory experiment showing that sexual conflict
might drive the rapid evolution of reproductive proteins.
95. Arnqvist, G., Edvardsson, M., Friberg, U. & Nilsson, T.
Sexual conflict promotes speciation in insects. Proc. Natl Acad. Sci.
USA 97, 10460?10464 (2000).
96. Metz, E. C., Gomez-Gutierrez, G. & Vacquier, V. D.
Mitochondrial DNA and bindin gene sequence evolution among allopatric
species of the sea urchin genus Arbacia. Mol. Biol. Evol. 15, 185?195
(1998).
Lilith
Nah, I define a request to jump through hoops to be the demand that I
repeat something I've already said. Talking about science NEVER seems
like an inconvenience, however...nothing like work. I type pretty
quickly, and I don't mind hitting my head off a brick wall for a few
minutes while I get to natter gleefully about stuff that's near and
dear to my heart.
lilith
Lilith
> charlie wagner <cha...@charliewagner.com> wrote in message
> news:ec838d5.02051...@posting.google.com...
> > Why does the gene for hemoglobin exist in a Vicia fava genome?
>
> Perhaps they need it for some purpose also, and its invention predated the
> animal/plant split. But more importantly - how similar is the legume hemoglobin
> to vertebrate hemoglobin? The fact that they're called the same thing does not
> imply that the proteins are structurally identical. A precursor organism with a
> globin-like gene that then diverged into animals and plants, with each lineage
> adopting the genes and diversifying them for its own purpose, is easily
> compatible with evolution.
Apparently there is a symbiotic relationship between Vicia Fava (fava
bean) and microbes in the root nodules. Fava provides the microbes
with oxygen as long as the microbes hang around. Symbiotic evolution,
how very neat.
There also exist non-symbiotic *globins in plants. I haven't looked
into the literature to see what they are but they seem to be several
that are well-known.
I've done the alignment of some various fava leghemolgobins (there are
apparently several) and hemoglobin itself in various animals. See this
link for the colorful alignment:
http://www-personal.umich.edu/~lilyth/heme.htm
As far as conservation goes, they look similar, but in truth they're
about 16% conserved between fava and human, as far as identity is
concerned.
Note that the 100% conservations among all the species are shaded in
color. Note also that in order for hemoglobin to function as an oxygen
storage mechanism, several residues have to be coordinating to the
iron, and from examination of the list I can see that many of the
conserved residues are probably either coordinating residues to the
iron atom (histidines (H) for example) or are structurally significant
(glycine "helix breakers" (G) for example). Etc. Any good webpage on
hemoglobin can explain the significance of the conservations among
these hemoglobins. Me, I'm going to bed. :)
lilith
oh and it's late at night, too.
George Acton
I once had a hemoglobin obsession and could do riffs on the
chains sliding for the Bohr effect. The clotting system can be
an obsession as well, but there is no Max Perutz of clotting.
When Mr. Wagner gets tired of your performance he will insult
you as a prematurely senile plodder and the kind of person who
persecuted Barbara McClintock and Peter Duesberg. But that's ok.
Scheherazade enjoyed her stories, and so do we.
--George Acton
Lilith
> There has been work with sea urchins, Drosophila, abalone, and other
> organisms to show that it's often not as simple as "sperm binds to
> egg". For example, there are several factors ('accessory gland
> proteins') that the male Drosophila includes with his sperm when
> mating with the female, including sperm competition factors (this
> isn't surprising, is it?). When one species of Drosophila, D. suzukii
> are crossed with D. pulchrella, they do not produce hybrid offspring
> UNLESS the D. suzukii females are provided with injections of
> accessory-gland extracts from D. pulchrella males. The
> species-specific accessory gland proteins are required for
> reproduction.
Late-night typo. I mean D. suzukii females need to be injected with
extracts from D. suzukii male accessory proteins in order to allow D.
pulchrella male sperm to fertilize their eggs.
Laurence A. Moran
charlie wagner <cha...@charliewagner.com> wrote:
[snip]
>You have no hope of convincing me that darwinism is the mechanism of
>evolution any more than you could convince me that there really is a
>Santa Claus who comes down the chimney on Christmas Eve.
Most of us have learned the hard way that it's hopeless trying to teach
you about biochemistry and molecular biology. Fortuntately for you there
are still a few suckers out there who continue to make the attempt.
Maybe this statement of yours will convince them that they are wasting
their time.
Larry Moran
Keith[bugeye]
"Bricklayer" <te...@moose-mail.com> wrote in message
news:Xns920E7AE4ED7...@130.133.1.4...
> mail1...@pop.net (Ferrous Patella) wrote...
>
> > In article <abprns$9c8$1...@helle.btinternet.com>, spandisman2
> > says...
> >>
> >>Just look at their attitude to the rest of humanity, what a load
> >>of ignorant arrogant anoraked tossers.
> >
> > 4.2 on a Mark V.
> >
> But I really like the part about "ignorant arrogant anoraked tossers"
>
> Brick
>
>
I would rather have a toaster
Dunk
see this article:
Ross Hardison:
The Evolution of Hemoglobin
An ancient protein proves to be an important part
of the evolutionary story
American Scientist March-April 1999, Vol. 87 No. 2
http://www.sigmaxi.org/amsci/amsci/articles/99articles/Hardison.html
and links from there.
Dunk
On Fri, 17 May 2002 06:09:47 +0000 (UTC), lil...@umich.edu (Lilith)
wrote:
Dunk
wrote:
>Gavin Tabor <G.R....@exeter.ac.uk> wrote in message news:<3CE3ADDF...@ex.ac.uk>...
That could be very useful. The usual method is to first post a draft
for discussion. Depending on length, you might post only a link here.
Dunk
Matt Silberstein
cha...@charliewagner.com (charlie wagner):
[snip]
>Darwinism is probably not falsifiable because it's almost impossible
>to prove that something didn't happen the way someone says it does.
>Added to that is the fact that the theory, as you described yourself,
>is basically whatever the individual says it is. The response is
>always "you don't understand evolutionary theory, it doesn't say that
>at all" If you attempt to define it before attacking it, you'll be
>accused of putting up a "strawman" argument.
Evolution, the process, is defined as the change in allele
frequency in a population of living organisms over time. Observed
consequences of this process include speciation and common
descent. The major known forces include imperfect reproduction,
differential reproductive success, and drift.
>No, the evolutionists
>have an answer for everything. And they're pretty good at it, since
>they've been defending this theory for over 100 years. But the
>creationists have called them out, and now the hoax is being exposed.
I think I will call you out and expose your hoax here. Let us
take one example: multiple drug resistant malaria. Millions of
people get sick from this each year, quite a few die. The actual
researchers use evolution as a major guide when then work on
dealing with this disease. What do you or the creationists offer
instead? Remember, quite a few lives are at stake here, you can
save millions, get world renown, get very rich, get remembered
for quite a long time. What specifically do you offer? Do you
have a thing or are you blowing smoke with your accusations?
>But organized science still has a great deal of political power and
>will use it when needed. It's a classic battle and it's been going on
>for thousands of years.
Really? Organized science has had this power for how long?
[snip]
charlie wagner
It's not hopeless to try to teach me about biochemistry and molecular
biology since there are clearly a great number of things that I don't
know about. And I welcome this kind of discussion. Lilith, for example
has made some valuable contributions to my understanding of how
molecular biologists view evolution and has also informed me of
several new and interesting things that I can look at, such as the
genomes of C. elegans and trypanosomes. These are the kinds of
feedback I hope to get from my postings and they are welcome and
appreciated.
On the other hand, what is hopeless is to try to undermine my views
on evolution and molecular biology by using scorn, ridicule, personal
attacks or other such inappropriate tactics without presenting factual
support for why you think I'm wrong. So, if anyone has something
worthwhile to offer, such as that presented by lilith and others,
those efforts will be graciously accepted and appreciated. And it will
not be a waste of their time.
So, I repeat my challenge, which has stood unanswered for lo these
many months (years). If anyone has any one single shred of credible
evidence that variation and selection has the power vested in it by
modern evolutionary theory, that is, the power to create new major
adaptations, processes, structures or organisms, they are welcome to
present it and it will be carefully and thoughtfully evaluated. In the
meantime, I will continue to view it in the context that I've always
viewed it: a just-so story and a "leap of faith"
Elmer Bataitis
> So, I repeat my challenge, which has stood unanswered for lo these
> many months (years). If anyone has any one single shred of credible
> evidence that variation and selection has the power vested in it by
> modern evolutionary theory, that is, the power to create new major
> adaptations, processes, structures or organisms, they are welcome to
> present it and it will be carefully and thoughtfully evaluated.
Charles Darwin, "On the Origin Of Species".
***************************************************************
Elmer Bataitis “Hot dog! Smooch city here I come!”
Planetech Services -Hobbes
585-442-2884
"...proudly wearing and displaying, as a badge of honor, the
straight jacket of conventional thought."
***************************************************************
charlie wagner
> In talk.origins I read this message from
> cha...@charliewagner.com (charlie wagner):
>
>
> [snip]
>
> >Darwinism is probably not falsifiable because it's almost impossible
> >to prove that something didn't happen the way someone says it does.
> >Added to that is the fact that the theory, as you described yourself,
> >is basically whatever the individual says it is. The response is
> >always "you don't understand evolutionary theory, it doesn't say that
> >at all" If you attempt to define it before attacking it, you'll be
> >accused of putting up a "strawman" argument.
>
> Evolution, the process, is defined as the change in allele
> frequency in a population of living organisms over time. Observed
> consequences of this process include speciation and common
> descent. The major known forces include imperfect reproduction,
> differential reproductive success, and drift.
Evolution is "change over time". You're mixing up 'evolution' and the
'mechanism of evolution'. Organisms change over time. The organisms of
today are different from those of the past. That's evolution. And it's
a 'fact' as you folks love to remind us. But variation and selection,
which result in changes in allelic frequency in a population under
selection pressure is a mechanism. And there's no evidence that it has
anywhere near the power that you think it has to create major
adaptations, processes, structures and organisms. Also, while common
descent may be a fact, it's not now and never has been, evidence for
natural selection.
>
> >No, the evolutionists
> >have an answer for everything. And they're pretty good at it, since
> >they've been defending this theory for over 100 years. But the
> >creationists have called them out, and now the hoax is being exposed.
>
> I think I will call you out and expose your hoax here. Let us
> take one example: multiple drug resistant malaria. Millions of
> people get sick from this each year, quite a few die. The actual
> researchers use evolution as a major guide when then work on
> dealing with this disease. What do you or the creationists offer
> instead? Remember, quite a few lives are at stake here, you can
> save millions, get world renown, get very rich, get remembered
> for quite a long time. What specifically do you offer? Do you
> have a thing or are you blowing smoke with your accusations?
Just showing that an organisms will develop drug resistance in
response to an environmental challenge is not now, and never has been,
evidence that this can lead in some way to new major adaptations,
processes or structures. We all know that mutations occur and other
changes in the genome occur. You have to show that these changes can
lead to something new.
>
> >But organized science still has a great deal of political power and
> >will use it when needed. It's a classic battle and it's been going on
> >for thousands of years.
>
> Really? Organized science has had this power for how long?
mad long....
Regards, Charlie Wagner
http://www.charliewagner.net
>
> [snip]
Don1
> john...@post.com (John) wrote in message news:<7a0afaa.02050...@posting.google.com>...
> > It's just common sense:
> >
> > 1. The scientific community would not accept evolution unless it were
> > soundly proved. As a theory, evolution (Darwin) is on par with plate
> > tectonics and the Big Bang. If origins of species were not understood,
> > singularities, time before the Big Bang, and life on other planets.
> > Science is not scheming against Christians.
> >
> > 2. Evolution has no baring on the existence of God, because He could
> > easily have created a universe complex enough to allow evolution to
> > proceed by natural law. The presence and manifestation of God in the
> > universe are not nullified by evolution.
> >
> > 3. Almost everything is evolving according to natural law: from the
> > expanding universe, to the death of stars, to the changing chemistry
> > of the Earth's atmosphere. Is life the only thing that doesn't evolve
> > by natural law -- requiring the continual "tinker toying" of God?
> >
> > Evolution is a simple, elegant theory, supported by the vast majority
> > of scientists, an extensive fossil record, genetics, geology, biology,
> > microevolution (laboratory and natural), and of course, common sense.
> >
> > John D. Callahan
> > Christian theistic evolutionist
> > http://www.faithreason.org/
>
> A brief perusal of the faithreason website revealed that the so-called
> divinity of Jesus was supported by his "resurrection." In other words,
> the claim is that because Jesus' body was not there after three days
> was proof that he resurrected and was therefore a god (whatever that's
> supposed to mean).
> Just asking: If Joe Shmoe (perhaps my noisy next-door neighbor)died
> and was buried three days ago but his body suddenly disappeared would
> his relatives be able to claim divine status for him? Or would some
> other conclusion seem more logical? Both the Romans and the Sanhedrin
> both had good cause to see to it that the followers of Jesus not have
> a rallying point in the form of Jesus' corpse. Conveniently enough,
> the guard slept through it all...
> The site also uses the tired arguments of Shroud of Turin advocates
> while ignoring evidence for its likely status as a fraud.
That is a strong statement. Can you list (in brief) the evidence that
points to the likelihood of the shroud being a fraud?
> In short,
> one could hardly recommend this site as useful support for TOE.
>
> Greg Czebatol
> Gregwrld (still waiting for evidence of creators and designers)
Matt Silberstein
cha...@charliewagner.com (charlie wagner):
>Matt Silberstein <mat...@ix.netcom.com> wrote in message news:<f7udeu4hd297oqhbi...@4ax.com>...
>> In talk.origins I read this message from
>> cha...@charliewagner.com (charlie wagner):
>>
>>
>> [snip]
>>
>> >Darwinism is probably not falsifiable because it's almost impossible
>> >to prove that something didn't happen the way someone says it does.
>> >Added to that is the fact that the theory, as you described yourself,
>> >is basically whatever the individual says it is. The response is
>> >always "you don't understand evolutionary theory, it doesn't say that
>> >at all" If you attempt to define it before attacking it, you'll be
>> >accused of putting up a "strawman" argument.
>>
>> Evolution, the process, is defined as the change in allele
>> frequency in a population of living organisms over time. Observed
>> consequences of this process include speciation and common
>> descent. The major known forces include imperfect reproduction,
>> differential reproductive success, and drift.
>
>Evolution is "change over time".
In the context of biology it is the specific change I stated
above.
>You're mixing up 'evolution' and the
>'mechanism of evolution'.
I clearly distinguished between the process, the results, and the
mechanisms.
> Organisms change over time.
Actually populations change.
> The organisms of
>today are different from those of the past. That's evolution. And it's
>a 'fact' as you folks love to remind us.
Only because those creationists you support deny this fact. I
say support because you assert they have "called" biologists on
the hoax of evolution. Denial of the fact of evolution is a big
part of what they see as this hoax.
> But variation and selection,
>which result in changes in allelic frequency in a population under
>selection pressure is a mechanism.
I called it a force, do you see a meaningful distinction between
force and mechanism in this context? If not, don't repeat what I
say as a way of correcting what I said.
> And there's no evidence that it has
>anywhere near the power that you think it has to create major
>adaptations, processes, structures and organisms.
Sure there is, lots and lots of such evidence. That you don't
find it persuasive does not make it go away.
>Also, while common
>descent may be a fact, it's not now and never has been, evidence for
>natural selection.
Of course not but I have not seen anyone claims it was.
>>
>> >No, the evolutionists
>> >have an answer for everything. And they're pretty good at it, since
>> >they've been defending this theory for over 100 years. But the
>> >creationists have called them out, and now the hoax is being exposed.
>>
>> I think I will call you out and expose your hoax here. Let us
>> take one example: multiple drug resistant malaria. Millions of
>> people get sick from this each year, quite a few die. The actual
>> researchers use evolution as a major guide when then work on
>> dealing with this disease. What do you or the creationists offer
>> instead? Remember, quite a few lives are at stake here, you can
>> save millions, get world renown, get very rich, get remembered
>> for quite a long time. What specifically do you offer? Do you
>> have a thing or are you blowing smoke with your accusations?
>
>Just showing that an organisms will develop drug resistance in
>response to an environmental challenge is not now, and never has been,
>evidence that this can lead in some way to new major adaptations,
>processes or structures.
IOW you have no alternative way of approaching the data, you have
no helpful ideas. You have just been blowing smoke about new
paradigms and new ways of looking at things.
>We all know that mutations occur and other
>changes in the genome occur.
Those creationist don't know this, so I wonder who this "we" is.
> You have to show that these changes can
>lead to something new.
How do you define "new"? Take the examples that gives
creationists the most trouble: humans and chimps. Do you think
there is anything "new" in the propose descent of humans and
chimps from a common ancestor? Do you find that path impossible
to achieve via mutation and selection? If not, what divergence do
you find impossible and why?
>>
>> >But organized science still has a great deal of political power and
>> >will use it when needed. It's a classic battle and it's been going on
>> >for thousands of years.
>>
>> Really? Organized science has had this power for how long?
>
>mad long....
Sorry, I must have missed that day in math class. How long has
this "organized science" had this political power?
Michael Painter
"Don1" <dina....@snet.net> wrote in message
news:56db0569.02051...@posting.google.com...
> GCze...@msn.com (Gregwrld) wrote in message
news:<c8df1ee6.0205...@posting.google.com>...
> > john...@post.com (John) wrote in message
news:<7a0afaa.02050...@posting.google.com>...
>
> points to the likelihood of the shroud being a fraud?
When the shroud was first "discovered" and at a time that the church was
making big bucks from relics one of the bishops to examine it declared it to
be a fraud.
"The Turin cloth first appeared in north-central France in the
mid-fourteenth century. At that time the local bishop uncovered an artist
who confessed he had "cunningly painted" the image. Subsequently, in 1389,
Pope Clement VII officially declared the shroud to be only a painted
"representation."
http://www.csicop.org/articles/shroud/index2.html
Vladimir Gritsenko
>
> 1. The scientific community would not accept evolution unless it were
> soundly proved. As a theory, evolution (Darwin) is on par with plate
> tectonics and the Big Bang. If origins of species were not understood,
> science would say so, just as it does concerning black hole
> singularities, time before the Big Bang, and life on other planets.
> Science is not scheming against Christians.
>
> 2. Evolution has no baring on the existence of God, because He could
> easily have created a universe complex enough to allow evolution to
> proceed by natural law. The presence and manifestation of God in the
> universe are not nullified by evolution.
>
> 3. Almost everything is evolving according to natural law: from the
> expanding universe, to the death of stars, to the changing chemistry
> of the Earth's atmosphere. Is life the only thing that doesn't evolve
> by natural law -- requiring the continual "tinker toying" of God?
>
> Evolution is a simple, elegant theory, supported by the vast majority
> of scientists, an extensive fossil record, genetics, geology, biology,
> microevolution (laboratory and natural), and of course, common sense.
>
> John D. Callahan
> Christian theistic evolutionist
> http://www.faithreason.org/
While I find it very respect-worthy when religion backs off in front
of science, I don't like mixing it together, because, by definition,
religion is about faith, and so it is irrational or unnatural. Science
is the opposite - it is (at least by today's definition) natural (not
everything makes sense, but it's there, whether it's very logical to
our human senses or not).
There are a few reasons for why I'm an atheist and don't like such
synthesis between religion and science (I take it as granted that God
can not be proved by natural or rational means):
(1) So many religions in this world, so many alleged truths. Which one
to believe? It's all nicely recorded and has applicable morals in it.
Monotheism is at the top right now, but we all know that the argument
of "let's assume that God is almighty and everybody are right" is very
contradictory. We must work very hard (and no matter how hard we work,
we'll always fail) to bridge the gaps. And these are just the 3
Abrahamic religions (I have close expirience with Judaism). What about
the rest of them?
(2) God was usually the best solution for the unknown. When man
couldn't explain something, he threw it at the supernatural. But
slowly explanations were arising, and so people had to abandon their
previous believes step by step. Now it came down to this: religions
can't use life, the most sacred and appreciated aspect of nature, as a
proof to God. A natural, plausible and supported by overwhelming
masses of evidence explanation exists (the theory of evolution). In
fact, even now, the only rational answer to such controversial
questions (like the "fine-tuning" of our world) is "we don't know".
But science constantly takes these questions on (and succeeds), and
this does NOT mean that an answer will never be found. And so, saying
"God exists" is equivalent to saying "I don't know" (if someone tries
to explain God rationally). It's also interesting to note that science
never needed the supernatural to explain any phenomenah.
(3) Contradictions in religion. I will give examples from the most
known religion to me, Judaism. This is, however, applicable to all
other religions. The truth about modern religions is that they are
contradictory. The Tanah needed so much explanation for statements
which sounded ridiculous and old, that religious wise men (apparently
aided by tradition passed down the generations and God himself) had to
write books (the Mishna, the Talmud, etc.) explaining everything by
mere story-telling. The most obvious contradictions are in such
statements of an all benevolent and forgiving God, but then we see
slavery, executions (for example, for not keeping the rules of
Sabbath), etc.
Another sub-paragraph is the question of how should we read the Bible,
or any other religious work. People seem to be very happy of reading
it as metaphore, but remember, it's only when it fits the current
moral and scientific point of view. Before the 15th century, the world
was literaly created in 6 days and evolution as we think of it simply
did not exist. Making nice stories and songs won't do. There must be a
simple standard for understanding this or that religious work, it must
be always uniform. However, it doesn't exist. And making it up won't
help the matter, as the question comes down to of whether every
generation before us was living in darkness and oblivion. I think that
everybody will agree that such a solution is not a solution, but a
cover-up.
(4) Advantages of faith. The advantages of faith (I can give you a
personal example - I'd sleep much more comfortably knowing that God
existed and that there is life after death and etc. I assume that my
life would be more comfortable if I was a theist) are very big, and if
a person is given a choice of either believing that he is devine or
that he emerged from slime (as Ted Holden quoted some cannibal), what
would you chose? If you would be presenetd with the opporunity to
believe life after death in heaven (the best place imagianable, of
course) or, simply put, nothingness, what would you chose? It is
simply a historic fact that religion held all known living societies
together, until secularism fell. And, religion is much better than
secularism to hold on to the power (not tested, but if we could, I'm
making an educated guess that it would be so). This just shows that
religion is not necesairly correct - it simply another human weakness.
These are my main reasons for not accepting any religious doctorine.
If one wants to believe in God, then I have nothing against it. But
having faith has very deep implications, which go much beyond the
personal psyche boost.
Ian Musgrave & Peta O'Donohue
Address altered to avoid spam, delete RemoveInsert
On Sun, 19 May 2002 16:39:40 +0000 (UTC), cha...@charliewagner.com
(charlie wagner) wrote:
[snip]
> So, I repeat my challenge, which has stood unanswered for lo these
>many months (years). If anyone has any one single shred of credible
>evidence that variation and selection has the power vested in it by
>modern evolutionary theory, that is, the power to create new major
>adaptations, processes, structures or organisms, they are welcome to
>present it and it will be carefully and thoughtfully evaluated. In the
>meantime, I will continue to view it in the context that I've always
>viewed it: a just-so story and a "leap of faith"
As I have said before, many people have given far more than "shreds"
of evidence, you just choose to ignore them.
Amongst this evidence is
1) Evolution of nylonase by deletion mutation in junk DNA
2) Evolution of the PCP hydrolysis pathway by duplication and mutation
of malate isomerase
3) Evolution of regulated ribitol hydrolysis
4) Evolution of a beta-galactosidase and it's control operon
5) Evolution of amide utilization
All of these involve the production of major new adaptions and
biochemical processes by mutation and natural selection, but you have
just had waved them away.
Cheers! Ian
=====================================================
Ian Musgrave Peta O'Donohue,Jack Francis and Michael James Musgrave
reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
Southern Sky Watch http://www.abc.net.au/science/space/default.htm
Andy Groves
> So, I repeat my challenge, which has stood unanswered for lo these
> many months (years). If anyone has any one single shred of credible
> evidence that variation and selection has the power vested in it by
> modern evolutionary theory, that is, the power to create new major
> adaptations, processes, structures or organisms, they are welcome to
> present it and it will be carefully and thoughtfully evaluated.
Can you give an example of a major new adaptation, process, structure
or organism that you have in mind?
Andy
howard hershey
----------
In article <ec838d5.02051...@posting.google.com>,
cha...@charliewagner.com (charlie wagner) wrote:
[snip]
> So, I repeat my challenge, which has stood unanswered for lo these
> many months (years). If anyone has any one single shred of credible
> evidence that variation and selection has the power vested in it by
> modern evolutionary theory, that is, the power to create new major
> adaptations, processes, structures or organisms, they are welcome to
> present it and it will be carefully and thoughtfully evaluated.
It might help if you gave us examples of what you mean by *new* major
adaptations, processes, structures, or organisms that 'evolution by
variation and selection' is unable to accomplish, given enough time and
repeated speciations. The reason I ask is because evolution does not, by
and large, produce novelties. It modifies existing structures, often to
such an extent that they are given new names and perform new functions. But
evolution rarely, if ever, produces true 'novelties', so I wonder what you
think evolution is. Evolutionary mechanisms never directly produce, in a
single step, new 'orders' or 'classes' or higher order divisions among the
currently living species. Creationism does that. Evolution produces
'higher order divisions' by multiple repeated speciation events and
extinctions. Evolutionary mechanisms produces closely-related species,
period. The creation of higher levels of classification linked by common
descent are a consequence of repeated speciation events, not a mechanism.
The rate of change in such evolutionarily important features as leg length
to body length, developmental rates, cranial capacity seen in the fossil
record, and the amount of genetically determined variance *within* currently
living species (all due, ultimately to random mutation) for various features
(especially the quantitative genetic traits most important for the types of
changes seen in evolution) and the rates at which allele frequencies can
change under selective pressure are quite compatible with evolution.
Indeed, it is quite clear that the amount of evolution that is occurring
under selective constraint is dwarfed by the amount of evolution that is due
to near neutral or selectively neutral processes. And evolutionary change
(base substitution) due to purely random processes is, in fact, dependent
upon random mutation rates.
> In the
> meantime, I will continue to view it in the context that I've always
> viewed it: a just-so story and a "leap of faith"
>
howard hershey
>
>
> >
> > Which HOX? There are several different HOX genes, some of which in
> > the HOX genes, too. That's not exactly a really good argument against
> > evolution, there.
> >
> > I also don't mean to sound too smarmy, here, but genes ARE conserved
> > between organisms. That's how we suspect we've got common ancestry.
> > But there are many genes which aren't in genomes like yeast or mouse
> > that we humans have. I can name several genes that are
> > primate-specific. Phorbolins 1, 2, 3, MORPHEUS, several HOX genes...
> >
> > But...let's go to the data! Let's pick one homeobox gene...you're
> > welcome to pick any. I'll randomly choose one, HOXB4. There are
> > several known orthologs cross-species to HOXB4 that are called HOXB4
> > in each species. Hopefully, if the classificion scheme works,
> > they'll all resemble one another discernably so we can see that they
> > do derive from an ancestral gene. Here's the breakdown (and you can
> > see the info at the following link:
That is the simplest explanation of the pattern of changes at the DNA
level. Specifically, genes that evolve from other genes by a pattern
of random mutation and either random drift or selection will show a
pattern of common descent that is in agreement with other patterns of
common descent.
> I maintain that we don't know the origin of genes at
> all, and we can't say that they came to be by a darwinian mechanism of
> evolution.
What do you mean by "the origin of genes"? The origin of hemoglobin
as a derivative of the similar myoglobin seems rather easy to explain,
as does the origin of beta-globin from alpha-globin. Are you under
the mistaken impression that "new" genes poof into existence from
random sequences?
> In fact we can't say anything at all about the origin of
> the genes. They could just have well come to the earth from elsewhere
> already containing the information that they use or they just as well
> may have been generated by other genomes by some sort of unfolding of
> an algorithm that was already present.
The extra-terrestrial origin has significant practical problems of
gaining specific entry into the appropriate organisms. And would
require a teleological goal for which there is no evidence at all.
Ditto for an "unfolding algorithm". Where is there any evidence at
all of a teleological process encoded into the DNA of organisms? That
would be a revival of the idea of the homunculus -- that all the
future generations of humankind were recorded in the eggs of Eve (or
the sperm of Adam).
> Evolutionists are seeing
> "relatedness" and they are automatically assuming an evolutionary
> explanation.
No. The specific *pattern* of relatedness of both DNA sequences and
the fossil record screams "common descent" of both molecules and
organisms. The *pattern* of common descent requires a mechanism, and
several rather easy extensions of mechanisms that can be observed in
the present (neutral drift and selection acting on continual
generation of variations) is more than adequate to the task.
> And this may well be because they are working from the
> premise that "evolutionary theory" is correct and therefore they may
> be explaining everything they see in the light of that pre-existing
> bias, rather than as new data. The fact is, IMHO, the fact that all
> living organisms are closely related is of profound significance, but
> that it says nothing whatsoever about their origins or their possible
> evolution.
So, what is your alternative explanation of the profoundly
'significant' and observed *pattern* of relatedness that we call
"common descent"?
> The only two things that we know for sure are that all
> living organisms are related and that the organisms that lived in the
> past are different from those that are extant today. Everything else
> is a deep mystery.
Well, perhaps to you. But the *pattern* of relatedness of both the
fossil and sequence record is rather easily consistent with common
descent which quite adequately explains the relatedness we see.
> But not knowing the origin of life doesn't mean we
> can't know how it works.
The 'origin of life' (aka, abiogenesis) is a different question, but
not one that really requires a rejection of 'common descent'.
> The research that is being conducted is
> important research, not so much because it can solve the mystery of
> our origins, but because by knowing how everything works, helps us to
> control and transcend it.
>
> >
> >
> > > and why can a complex process like photosynthesis
> > > be traced back to the very beginning of life on earth.
> >
> > That's not even a tough one to answer. We all apparently have the same
> > metabolic toolbox from that point in time, too. Where else, but in a
> > billion years of a population of rapidly reproducing and highly
> > competitive microorganisms would you get the opportunity to evolve
> > life as we know it? I rather like to imagine that hemoglobin, and most
> > of the porphyrins, stemmed out of some form of ancient chlorophyll
> > ancestor. It's funny how similar chlorophyll, hemoglobin, and
> > cobolamine are in structure and mechanism, and how they're different.
>
> Yes, I was astonished myself when I first examined the chemical
> structure of hemoglobin and chlorophyll. In fact, in the old days :-)
> I was one of the only people in my group to champion the work of Lynn
> Margulis when people were saying she was a crackpot. I always had a
> strong attraction to the radical thinkers and the crackpots.
I can see your strong attraction to crackpottery. There is a
difference between crackpottery (your ideas) and the ideas presented
by radical thinkers in science that you have yet to figure out.
> They are
> often the source of the best thinking. You can put that example under
> my list of "weirdnesses". Anyway, I think it's pretty clear (to me
> anyway) that photosynthesis didn't 'evolve" here on earth from the
> primordal ooze.
And your evidence is? The fact is that organisms that do not undergo
photosyntheses at all use a significant fraction of the biochemical
pathway of photosynthesis and extract energy from chemicals. There
are even bacteria that can grow given only iron pyrite, CO2, N2, and
very acidic water.
> Rather, I think it's highly likely that it came to
> earth from elsewhere already to go. The oldest stromatolites go back
> at least 3.45 billion years. That doesn't give very much time for it
> to evolve. But just look at those molecules. The argument from
> incredulity makes a very strong case that this is no accident.
>
Buckyballs are also complex structures, but all it takes to create
them is heat and appropriate carbon sources.
> >
> > >On a macro
> > > level, there are countless questionable observations that dispute
> > > darwinism. The gaps between classes that shouldn't be there.
> >
> > Such as? Give me some specifics, here.
>
>
> Well, I don't want to get into a whole thing about transitional forms,
> that's a bottomless pit if ever there was one. Suffice it to say that
> the fossil record tells us almost nothing about the evolutionary
> origin of phyla and classes.
It tells us that the differences between *modern* classes (or higher
groupings) arose when there was significantly less difference between
the diverging groups.
> Intermediate forms are non-existent,
> undiscovered or not recognized. Ask any paleontologist.
>
For *some* (especially creationist) definitions of "intermediate",
that may be true. For definitions that paleontologists use (an
organism with diagnostic features of two or more modern group's
identifying features),there are many 'intermediate forms', from groups
as diverse as whales to birds to great apes in the hominid lineage. So
what erroneous definition of 'intermediate' are you using?
> >
> > > The
> > > sudden appearance of all of the known animal phyla in a very short
> > > time and the appearance of no new phyla over the next 500 million
> > > years.
This is both false and true. Phyla, of course, represents the deepest
and *necessarily* oldest divisions among living groups. That puts
most phyla origins at a point earlier than the first hard parts that
are easily fossilizable.
> >
> > Someone could remind you here that the fossil record is necessarily
> > incomplete. But I don't have to do that, do I?
>
> After 142 years of looking by plenty of grad students and post-docs,
> one would expect that at least one example of *most* extinct forms
> would have been found. A large percentage for sure.
This is a repeated statement of willful ignorance on your part that
has been corrected time and time again. We *know* that the fossil
record is biased. We *know* the types of conditions that favor
fossilization and *know* than most organisms do not meet those
conditions (hard parts, rapid burial, no major episodes of heat and
pressure in the sediments). We *know* that the completeness of the
fossil record gets worse with age.
> There are god
> knows how many millions of living forms, I don't know the number
> exactly, we have far fewer extinct forms represented than extant
> forms. It ought to be the other way around, shouldn't it?
>
Given the rarity and biases in fossilization, it is lucky that we have
as good a record as we do. One that, although incomplete, often (in
at least some lineages) provides sufficient data points to draw a
reasonable line of best fit.
> >
> > >The fact that the fossils of the Burgess Shale and the fossils
> > > of the Chengjiang region show no significant differences despite the
> > > fact that they are separated in time by 40 million years, in a time
> > > when evolution was allegedly proceeding at a very rapid rate.
> >
> > Define "no significant difference", and I'd like some scientific
> > references, please.
>
> "Fossilized Soft-bodied Fauna", Chen Jun-Yuan, Jan Bergstrom and Hou
> Xiangguang
> National Geographic Research and Exploration, Winter 1991
>
> An exerpt from his conclusion:
>
> "In fact, evolutionarily, the Chengjiang arthropods
> are not much different from those of the Burgess Shale, despite their
> distinctly older age, and, hence, do not bring us much closer to the
> origin
> of arthropods, at least not from a morphological point of view.
> Part of the importance of the Chengjiang fauna mav lie in the
> implication
> that the initial coelomate radiation was extremely rapid and
> morphologically far-reaching. The Middle Cambrian Burgess Shale fauna
> shows several of the animal phyla we meet in the seas today.
> A step back in time some tens of millions of years brings us to the
> Early
> Cambrian Chengjiang fauna. During this time span, evolution seems to
> have produced very little change."
>
The above does not support your position.
>
> >
> > > Anyone who takes the time to think about this with an open mind
> > > and just looks casually at the actual evidence cannot help but discard
> > > this theory immediately. I don't believe in darwinism for the same
> > > reason that I don't believe in the tooth fairy. Or god.
> >
> > I beleive in darwinism because I play with its consequences every day.
> > I suppose I could have an "open mind" and be ready to accept any other
> > theory that comes along, but Darwinism is how I, and the company I do
> > research for, gets results (see above methods for a small smattering).
>
> Darwinism is a mechanism, based on variation and selection. There is
> no question that mutations occur and there is no question that
> selection can change the frequencies of alleles in populations. What
> is lacking is evidence that these trivial effects can produce major
> adaptive changes, new structures and processes and new organisms. With
> all due respect, and feel free to correct me if I'm wrong, it would
> appear to me that this question regarding the creative power of
> darwinism is not something that enters into your daily activities.
Are you including the powerful impact of gene duplication? And do
remember that most evolution (the vast majority) does not involve
single events that produce 'major adaptive changes, new structures and
processes and new organisms'. Evolution involves a step-wise process
of modifying structures and processes and organisms until they exhibit
differences large enough to be called "new". Most of these
differences represent modifications of previously existing structures
and processes (vide, wings and hemoglobin). Novelty from sheer
randomness is not the usual evolutionary mechanism.
>
[snip]
>
> When I got married in 1965, I moved out of my house and took my
> own place. My mother, in her usual fashion, threw out everything that
> I had left behind which she deemed to be "junk". Among that stuff was
> my proudest possession, a letter from Isaac Asimov that I received in
> reply to a query about flying saucers. He lambasted me for being such
> an idiot and reminded me that only a complete moron could ever believe
> in flying saucers.
He was correct. You were drawn to crackpottery even then.
> Later, in the middle 70's I attended the National
> Science Teachers Convention in Chicago and there were two keynote
> speakers on the same day. Sagan in the morning and Asimov in the
> afternoon! After the talk, I engaged Asimov in conversation and told
> him the story. He found it amusing and took my address, saying he
> would write another note for me. He never did. But I felt terrific
> about the conversation, especially the part where he remembered my
> father's candy store on Kings Highway in Brooklyn.
[snip]
>
> Now, if you're looking for weirdness, here's an adult portion.
> Why should the molecular data show divergence times that considerably
> pre-date the paleontological record? One of them is wrong.
Yep. That is the way science works. There are similar examples of
such a discrepancy. In some cases, the fossil record was incomplete
and new fossils in the appropriate layers demonstrated this. In
others, there is in fact reason to believe that the rates of evolution
in some lineages is faster (or slower) than in others.
Scientists search diligently for mechanisms that can produce genetic
variation. The *only* ultimate source of genetic variation that was
found is mutation and every example of mutation we know about occurs
by mechanisms that do not act in a teleological fashion. So it is
hardly for lack of trying that we conclude that mutation that occurs
randomly wrt need is the source of variation in genomes.
Selection and the impact of selection on genetic variation has also
been studied extensively. *When* it occurs, it produces changes in
allele frequency that is both rapid and powerful. *When* selection
does not occur, there are selectively neutral mechanisms that also
produce evolutionary changes in genomes. The evidence clearly points
out that changes in genomes due to selection is an insignificant
fraction of the genetic differences between organisms (except when due
to duplication and divergence) and that the amount of sequence
differences between organisms can often be simply be due to neutral
processes. Comparing the structure of genomes also points out the
powerful role of duplications, chromosomal rearrangements, and
transposition events in evolutionary divergences. AFAIK, all the
differences in the genomes of organisms are largely consistent with
the amount of time since divergence.
> >
> > > > By the way, the only conspiracy supporting evolution is the conspiracy
> > > > of evidence supporting it.
> > >
> > > To save some time, I'd be happy with just *one* piece of solid
> > > evidence.
First you have to tell us what you mean by "novelty"? Then we can
tell you whether or not such a "novelty" is consistent with known
mechanisms and rates of change. Choose a novelty that has some fossil
or DNA evidence that can allow one to test between alternative
hypotheses. Don't choose an example where the absence of any possible
evidence you would accept allows you to claim that your personal
ignorance favors the choice you make in ignorance.
> >
> > I gave you a few up above. I suppose you could reduce them all
> > absurdly to "circumstantial" but if you resort to that, I hold that
> > you will never be convinced one way or another.
>
> The evidence you offer reinforces the already accepted notion that all
> living organisms are related
Yes they are. But you tell us what kind of *pattern* of relationship
one sees in the fossil record.
> and that changes can occur in genomes by
> a variety of methods. What your evidence does not estanblish, is a
> nexus between changes in the frequencies of alleles in populations
> under selection pressure, and new major adaptations.
What "new major adaptations"? How do you recognize a "new major
adaptation" from an adaptation with intermediate states one can see
(and place a rate of change on) aside from choosing places where there
is no evidence? Let's look a fossil lineage that is relatively
complete -- say forams. Where in the foramniferan lineage do you see
a "new major adaptation"? Or, say the 'horse' bush. Is switching
from browsing to grazing a "new major adaptation"? Is a change in
foot structure a "new major adaptation"? Is the change in cranial
size in the hominid lineage a "new major adaptation"? Or do you only
see "new major adaptations" in lineages where there is no evidence
that could answer the question?
> >
> > > > I'm prepared to start citing references. Are the creation scientists
> > > > ready to start debating real data?
> > >
> > > And I'm prepared to listen to whatever you have to offer. But be
> > > careful to produce evidence that mutation and natural selection is the
> > > mechanism of evolution, not simply evidence that living forms changed
> > > or that they're related.
> >
> > Read Eichler's segmental duplication articles above, if you can get
> > them. He shows the appearence of neurological genes unique to primates
> > which then diverge with strong evidence of positive selection. He also
> > shows that this kind of positive selection is apparent in what
> > evolutionists consider the strongest candidates for rapid evolution:
> > reproductive genes, xenobiotic genes, and predator/prey competition
> > genes. This, of course, is only one example. But you really have to
> > take the time to read the articles to understand the implications of
> > genetic-material swapping wholesale among the chromosomes.
>
> Do you really believe for a second that the higher neurological
> function found in the human brain, the complex and subtle ability to
> make abstractions and to solve problems, the musical and artistic
> ability, the language skills and the emotions were the product of
> random fortuitous errors in the genomes and selection pressure? You
> might as well believe that the moon is made of green cheese.
>
What evidence do you have that such a change in higher function
requires something more involved than random fortuitous errors in
gene(s) followed by selection. How many *selectively important* gene
changes do you think you need to make to produce the human brain from
an ancestral chimp-like brain? An order of magnitude guess is in
order. My guess would be significantly less than 100. Perhaps even
less than 10. With many of those differences only having an
(individually) modest effect.
> >
> > If you can't believe this kind of smoking gun, you can't ever be
> > convinced, unless you can actually provide the readers with a
> > classification or explanation of something that would convince you.
>
> Nothing, I'm afraid, will ever convince me that evolution proceeds at
> the direction of random, fortuitous mutations and natural selection.
> Sorry.
>
That is because that is a religious belief you have, not a scientific
position. Your real objection seems to be that evolution appears to
be completely non-teleological because mutation is not sent down to
earth from some extraterrestrial source to solve problems that some
extraterrestrial something wanted to solve. That there seems to be no
unfolding of a teleological plan and no mechanism by which such a
teleological change process can occur.
>
> >
> > >
> > > Regards, Charlie Wagner
> > > http://www.charliewagner.com
> > >
> > > >
Jack Dominey
> If anyone has any one single shred of credible
> evidence that variation and selection has the power vested in it by
> modern evolutionary theory, that is, the power to create new major
> adaptations, processes, structures or organisms, they are welcome to
> present it and it will be carefully and thoughtfully evaluated.
In the absence of a useful definition of "major adaptations,
processes, structures, or organisms" (a *definition*, mind you, not a
wad of examples) - a definition that others can understand and apply
without having to ask you first - your 'careful and thoughtful
evaluation' looks suspiciously like prejudicial handwaving.
By the way, don't you appreciate the way your own comments on the
integration of the genome just destroy the 'genes from space'
speculation?
Jack Dominey
elvon is a spamtrap
jack_dominey (at) email (dot) com
howard hershey
In article <ec838d5.02051...@posting.google.com>,
cha...@charliewagner.com (charlie wagner) wrote:
[snip]
> So, I repeat my challenge, which has stood unanswered for lo these
> many months (years). If anyone has any one single shred of credible
> evidence that variation and selection has the power vested in it by
> modern evolutionary theory, that is, the power to create new major
> adaptations, processes, structures or organisms, they are welcome to
> present it and it will be carefully and thoughtfully evaluated.
It might help if you gave us examples and a definition of what you
mean by *new* major adaptations, processes, structures, or organisms
that 'evolution by variation and selection' is unable to accomplish,
given enough time and repeated speciations. The reason I ask is
because evolution does not, by and large, produce novelties. It
modifies existing structures, often to such an extent that they are
given new names and perform new functions. But evolution rarely, if
ever, produces true 'novelties', so I wonder what you think evolution
is. Evolutionary mechanisms never directly produce, in a single step,
new 'orders' or 'classes' or higher order divisions that we see among
the currently living species. Creationism does that. Evolution
produces 'higher order divisions' by multiple repeated speciation
events and extinctions over geological time frames. Evolutionary
mechanisms produces closely-related species, period. The creation of
higher levels of classification linked by common descent are a
consequence of these repeated speciation events, not a mechanism in
and of itself.
The rate of change in such evolutionarily important features as leg
length to body length, developmental rates, cranial capacity seen in
the fossil record, and the amount of genetically determined variance
*within* currently living species (all due, ultimately to random
mutation) for various features (especially the quantitative genetic
traits most important for the types of changes seen in evolution) and
the rates at which allele frequencies can change under selective
pressure are quite compatible with evolution.
Indeed, it is quite clear that the amount of evolution that is
occurring under selective constraint is dwarfed by the amount of
evolution that is due to near neutral or selectively neutral
processes. And evolutionary change due to purely random processes is,
in fact, clearly dependent upon and estimated by random mutation rates
(the rate of neutral substitution is the same as the rate of mutation
for selectively neutral sites).
> In the
> meantime, I will continue to view it in the context that I've always
> viewed it: a just-so story and a "leap of faith"
>
wf...@ptd.net
(charlie wagner) wrote:
>I am familiar with the work being done in the Eichler lab and others,
>including Susan Rosenberg at Baylor. People are beginning to look at
>the genome a little bit differently now, and that's good. The "hoops
>of steel" that bound us to the darwinian paradigm are being loosened
>and gradually a new paradigm is emerging, one in which the genome is
>seem in a more dynamic and adaptive light. Those who insist on
>clinging to the old paradigm and who continue to try to shoehorn these
>new discoveries into the old molds will be left behind.
of course, folks have been saying this about darwin for 150 yrs...
> Barbara McClintock said in her Nobel laureate address "the genome
>is a highly sensitive organ of the cell, that in times of stress could
>initiate it's own restructuring and renovation". A far cry from the
>concept of random, fortuitous mutations.
as a chemist, seeing the genome in a chemical context, one can only
wonder at the original quote from which this has been culled...
---------------------
"This difference between liberalism and conservatism
must not be obscured by the fact that in the United
States it is still possible to defend individual
liberty by defending long-established institutions.
To the liberal they are valuable not mainly because
they are long established or because they are
American but because they correspond to the
ideals which he cherishes."
F. A. Hayek in "Why I am not a Conservative"
Bigdakine
>From: dina....@snet.net (Don1)
>Date: 5/19/02 5:06 PM Hawaiian Standard Time
>Message-id: <56db0569.02051...@posting.google.com>
You mean besides the fact that it Carbon dates to the 12th century or there
abouts?
Stuart
Dr. Stuart A. Weinstein
Ewa Beach Institute of Tectonics
"To err is human, but to really foul things up
requires a creationist"
Wayne Bagguley
> Re: Evolution for Dummies and Christians
>
> snow...@snowbird.freeserve.co.uk (Wayne Bagguley)
>
> Heyd...@webtv.net (Tom McHale) wrote in message
> news:<28050-3CE...@storefull-2315.public.lawson.webtv.net>...
>
> Extraordinary claims require extraordinary evidence. Admittedly as yet I
> have no specific explanation for this background radiation except that
> it may be local, a possible combination of sources.
>
> The big bang must be viewed in it's entirety relative to any specific
> aspect.
>
> >What does that piece of verbal diarrhoea mean? <
>
> It means that you cannot arbitrarily attribute a phenomenon to suit the
> purposes of your desired conclusions.
That's precisely what you are doing - arbitrarily attributing the
background radiation phenomenon to suit the purpose of your desired
conclusions.
> Credulity is stretched well beyond the limits of reason by the big bang.
And your reason for reaching that arbitrarily chosen conclusion is?
> >It's only your personal incredulity that's the problem<.
>
> Prove all things. I stole this from the Bible.
Prove that god exists then.
> It requires more faith as does evolution than any religion organized or
> not
Prove it.
> >Are you claiming that there are levels of faith? Please tell me the
> definition of faith you are using and how you measure the various levels
> of it.<
>
> I take very good care of my two Suburbans with emphasis on items of
> safety especially the brakes therefore when I apply the brakes, I have
> faith that the vehicle will stop. You might call this rational faith but
> then again that is a rather blatant contradiction in terms so let us
> call it rational expectations, sounds like a very good title for a movie
> Now for the more commonly accepted definition of faith as exemplified
> by a brown baby floating down the Nile, the precursor to Charlton
> Heston, his descendent who went into business for himself and did quite
> well, a delusional, ranting, hallucinating camel jockey, based on the
> preceding, my faith meter registers zero.
Exactly which drugs are you taking?
> and of course we are all aware that faith is an irrational concept.
>
>
> >So I can presume that you don't have any faith then? <
>
> Only as clearly expressed by the above paragraph.
Which wasn't clear at all.
> Let us be rational.
>
> >I am being rational. You are the one who is being irrational. You state
> quite clearly that you "have no specific explanation for this background
> radiation except that it may be local, a possible combination of
> sources"
>
> If you have no explanation then how is it rational to conclude that it
> may be local? In the total absence of any evidence, your explanation is
> simply an irrational assertion based entirely on faith. <
> -
> Wayne <
>
> I have not stated localization as a fact, I am speculating 'theorizing'
> and I have clearly stated this fact. And I also do not have what I would
> consider a complete viable theory of quantum gravity however I am making
> progress. Stay tuned.
Do they let you out of the asylum often? Seriously, do you really think
that you can formulate a theory of quantum gravity? What university are
you performing the research at? What does Professor Hawkins think about
your work? What evidence do you have that leads you to even think about
starting to theorise about the background radiation being a local
phenomena? What drugs are you on?
-
Wayne
Gregwrld
Sorry it took so long to get back to this.
According to a report written by Pierre D'Arcis 1389 for Pope Clement
the VII:
"Eventually, after diligent inquiry and examination, he (speaking of a
predecessor)discovered the fraud and how the said cloth had been
cunningly painted, the truth being attested by the artist who painted
it, to wit, that it was a work of human skill and not miraculously
wrought or bestowed."
As a result, the Pope allowed the cloth to be exhibited with the
announcement that "it is not the true Shroud of Our Lord, but a
painting or picture made in the semblance or representation of the
Shroud" (Humber, 1978, 100)
In 1973, a secret commission appointed by the Archbishop of Turin
tried to validate the "blood" on the "shroud". Unfortunately for
shroud advocates "all of the microscopical, chemical, biological, and
instrumental test were negative...Experts discovered reddish granules
that would not even dissolve in reagents that dissolve blood, and one
investigator found traces of what appeared to be paint." (Nickell)
Microanalyst Walter McCrobe, investigating on behalf of shroud
advocates, analyzed 32 samples from the shroud and found that the
so-called "blood" was "tempura paint containing red ochre and
vermillion along with traces of rose madder - pigments used by
medieval artists to depict blood." (Nickell)
There is considerably more evidence against the authenticity of the
shroud, and evidence for fraud by its advocates. I'm indebted to
CSICOP investigator Joe Nickell and his article in the
September/October 2001 issue of Skeptical Inquirer for this
information. Before any shroud advocates submit further claims here, I
suggest they obtain a copy of the article (perhaps through:)
Greg Czebatol
Gregwrld (seemingly surrounded by superstitious baloney)
Don1
So the scientific evidence that you list is the testimony of a bishop
and the fact that a pope made some statement about it in 1389? That is
hardly convincing or scientific.
I read through the URL you have provided and the information is very
one-sided. There is other conflicting information out there, too, which
should not be excluded from a scientific analysis.
For example, I recommend that you take a look at the book
The Jesus Conspiracy by Kersten and Gruber
Noelie S. Alito
Does that book address the samples of the shroud's "blood" which
turned out to be paint...of a type used in the 14th century?
(Personally, I was surprised at that discovery, since I thought it
would be trivially easy for hoaxers to get real blood--even
human blood--and would not need to resort to paint.)
[Hmm.... What would scriptural literalists say about a shroud which
does not match the description given in the gospels? Calling all YECs!]
Noelie
--
"Rhyming with 'goalie' for over 42 years."
Don1
You are of course referring to the mass spec experiment done by Gove
et al. I do not think that this is an established fact, since (1) the
results are not reproducible. And (2) earlier claims of scientific
experiments demonstrated that the shroud was around 2000 years old.
Of course, you could claim that the earlier experiments were biased.
But really so was the later one. If you read "Relic, Icon or Hoax.
Carbon Dating the Shroud of Turin" by Gove, you can actually see the
bias.
As to the reproducibility of results, is not that a cornerstone of
science? Let us suppose that Gove claimed the Shroud was 2000 years old.
Let us suppose also that he had written down a bunch of supporting numbers
and then later wrote a book about it. If later, he told you that you
could not reproduce the results, would you believe him? If an additional
two labs supported Gove's results, but were in part funded by the same
organizations, would you then believe the results? What if you still
could not reproduce the results yourself? Are you going to rely on
three testimonies?
Don1
Literary Points:
Some of your information might work in a persuasive essay, but not in
real science. I frankly do not care what a religious figure in 1389
declared based upon an alleged confession of an unknown hoaxer. And I
further do not think it adds to the scientific analysis at all.
Scientific Points:
I guess you think that Gove has actual evidence and that STURP was a
conspiracy. How do you intend to disprove the primary alternative
hypothesis: that Gove was involved in a conspiracy and that STURP had
actual evidence? I ask this, since neither you nor I can reproduce any
of the experiments which were done on actual shroud sample.
TomS
<acf3o8$p921c$1...@ID-117948.news.dfncis.de>, "Noelie stated..."
[...snip...]
>[Hmm.... What would scriptural literalists say about a shroud which
>does not match the description given in the gospels? Calling all YECs!]
Are you wondering whether a scriptural literalist/YEC is bothered
by inconsistency?
If so, the answer is "no".
Tom S.