Your comment "The present understanding of gene change can be briefly
stated as 'Cut, Copy, Paste.'" refers to transposons, which can cause
mutations:

http://users.rcn.com/jkimball.ma.ult...ansposons.html
http://users.rcn.com/jkimball.ma.ult...Mutations.html

Therefore, it seems you are agreeing with my statement that "genes and
alleles do arise by chance via mutation."

I still don't see how you can disparage one definition of evolution
without explaining why and yet will not provide a definition you
consider satisfactory. Your statement that the evolution definitions
"confuse measurement with definition" is a bogus argument. Measuring a
change in allele frequency is not at all like "measuring individual
body weight" as you suggest. Human body weight is largely a function
of environment, not genetics.

I don't see that you have any basis for criticizing the American
education system when you can't even provide a definition for
evolution.

Again, you are still confusing homogeneity and homozygosity. One
reason why Coffea arabica is disease susceptible might be its
homogeneity but that does not necessarily have anything to do with its
homozygosity. A homozygous crop can be very disease resistant if it
has the required disease resistance alleles. Too, heterozygous crops
are often homogeneous, which increases their disease susceptibility.
For example, in 1970, most of the hybrid corn cultivars in the United
States had the same genes for Southern corn leaf blight susceptibility
resulting in a devastating epidemic for that disease.

You stated "As I stated a few posts back you will have to find another
source to continue your education on the evolution of plant diseases."

If you are implying that I view you as a source of education on
evolution of plant diseases, you have proved that false time and time
again because you provide no facts or references to support your
hypotheses. I mainly end up just pointing out your errors. It appears
that you either know very little or don't want to share your vast
knowledge because you will not answer any of the questions I have
posed, e.g.

1. "What is your definition of evolution if you disagree with the
definition I presented, i.e. ."...evolution can be precisely defined
as any change in the frequency of alleles within a gene pool from one
generation to the next.""

2. "Based on your contention that "extra genes/alleles have additional
effects" how do you explain that C. arabica with 44 chromosomes is
more disease susceptible than C. canephora with just 22?"

3. "...your hypothesis that homozygous species or cultivars will be
more disease susceptible than heterozygous species and cultivars. Is
that just something you thought up yourself or is there a website,
book or reference where you got the hypothesis from?"

David R. Hershey



"P van Rijckevorsel" wrote in message ...
David Hershey wrote

If chance mutations don't give rise to new alleles in plant species,
then how do they arise? Many alleles do not code for "normal" or
functional proteins. The explanation is that the abnormal alleles
arose via mutations in the existing normal allele.

+ + +
It is a truism that our understanding of how 'nature' works keeps pace with
the development in the technology surrounding us. For example human brain
functions were once compared with cog-and-gear systems and are now likened
to computers. The present understanding of gene change can be briefly stated
as "Cut, Copy, Paste"

Note that not all genes code for proteins.
+ + +

You stated "Glad to see these two sites contradicting each other, when
it comes to (mis)defining evolution ;-) Although it remains sad to see
evolution so poorly taught".

You cast aspersions on the two evolution websites I cited but give no
substantive reasons why you berate them. If you find they contain
inaccuracies why not point them out to justify your criticisms? What
is your definition of evolution if you disagree with the definition I
presented, i.e. ."...evolution can be precisely defined as any change
in the frequency of alleles within a gene pool from one generation to
the next."?

Notice that the definition does not include natural selection because
it is not absolutely required for evolution to occur, although natural
selection very often does cause evolution. Allele frequency can change
without natural selection due to genetic drift:
http://www.talkorigins.org/faqs/genetic-drift.html

+ + +
There are two major things wrong with these "definitions":
- firstly they confuse measurement with definition. You can try and measure
the progress of evolution by measuring gene / allele change. That is not
evolution but only one way of measuring it. It is like expressing human
progress over the last millenia by measuring individual body weight: this
may be be useful data but presents only a small part of the picture.
- secondly it says nothing about evolution: if you replace the word
"evolution" by "genetic change" you can put this 'definition' into just
about any Creationist textbook without anybody raising an eyebrow

I had heard that the American educational system had gone to hell but if
this is part of any textbook actually used in schools it is much worse than
is usually sketched. I can only hope that the website presents it out of
context.
+ + +

You stated, "You also emphatically stated several times that of any
one gene only one version was active, at least distinctly implying
that you held an alternate theory on why polyploids often have
"greater vigor than diploids", since you so heavily discount the
obvious explanation that the extra genes / alleles have additional
effects."

I never said that "of any one gene only one version was active" always
occurred. I only said that when you have a heterozygous condition, the
recessive allele often codes for no protein. I even gave an example
from Mendel's wrinkled/smooth peas.

I pointed out last time that Coffea arabica is a tetraploid with 44
chromosomes and C. canephora is a haploid with 22 chromosomes. Based on your
contention that "extra genes/alleles have additional effects"
how do you explain that C. arabica with 44 chromosomes is more disease
susceptible than C. canephora with just 22?

+ + +
Coffea arabica is particular susceptible to a new disease developing since
it is a crop that is both homozygote and homogeneous.

I assumed you had caught that by now?
+ + +

After all these posts, you still have provided no evidence beyond one
example for your hypothesis that homozygous species or cultivars will
be more disease susceptible than heterozygous species and cultivars.
Is that just something you thought up yourself or is there a website,
book or reference where you got the hypothesis from?

David R. Hershey

+ + +
As I stated a few posts back you will have to find another source to
continue your education on the evolution of plant diseases.
PvR

===============================

"P van Rijckevorsel" wrote

David Hershey wrote
Chance is an important part of evolution because genes and alleles do
arise by chance via mutation. Your own Hugo de Vries brought the
concept of mutation into the Theory of Evolution. Without the genes or
alleles provided by mutation, natural selection would have nothing to
select for. Even clones, such as apple cultivars, often produce
favorable mutations that result in new improved cultivars.

+ + +
Actually there has been progress in science since Hugo de Vries,
and it is pretty clear that mutations as such are not really the factor they
were made out to be, unless one takes the position that any change in the
genome is a mutation, which would be a self-redundant statement. How long it
may last till the lay public realizes this is another matter. Creationism
certainly does not help.

As I have been trying to make clear there is a difference between
species and cultivars. The fact that 'mutations' occasionally give rise to
new cultivars has little bearing on what happens in species. The common link
between species and cultivars are that they arise through selection, but
both method and purpose of these respective forms of selection are greatly
different.
+ + +

I did say that natural selection was responsible for changing the
frequency of alleles and genes. A change in the frequency of a gene or
allele in a population results in evolution. It not uncommon to define
evolution that way, e.g."...evolution can be precisely defined as any
change in the frequency of alleles within a gene pool from one
generation to the next." -
http://atheism.about.com/library/glo..._evolution.htm

There are also other factors besides natural selection that cause
evolution: http://www.ucl.ac.uk/~ucbhdjm/course.../OneGenePP.pdf

+ + +
Glad to see these two sites contradicting each other, when it comes to
(mis)defining evolution. ;-)

Although it remains sad to see evolution so poorly taught
+ + +

The frequency of an allele often changes due to natural selection. For
example, suppose one mutation in one plant gives rise to an allele X
providing resistance to an often lethal disease. If that disease
occurs widely in the population, then plants with the X allele will
survive at a far greater rate than those without allele X. Thus, most
plants of the species will eventually carry the X allele so its
frequency increases greatly.

Stop putting words in my mouth again, I presented no "alternative
theory on polyploids". I don't dispute that polyploids often have
greater vigor than diploids. However, that tends to contradict your
hypothesis given that C. arabica is a tetraploid with 44 chromosomes,
and C. canephora is a diploid with 22.

+ + +
You also emphatically stated several times that of any one gene only one
version was active, at least distinctly implying that you held an alternate
theory on why polyploids often have "greater vigor than diploids", since you
so heavily discount the obvious explanation that the extra genes / alleles
have additional effects.
+ + +

The key dispute has been your unsupported hypothesis that homogygous
crops are more disease susceptible than heterozygous crops simply because
they are homozygous. The only example you cite is homozygous Coffea arabica
being more susceptible to disease than heterozygous C. canephora. However,
that could be due to poor breeding or poor selection of C. arabica
cultivars. It could also be that C. arabica by
chance simply has fewer disease reistance genes or alleles than C.
canephora. You have yet to provide any evidence that the homozygous status
of C. arabica has anything to do with is greater disease susceptibility.

David R. Hershey

+ + +
Actually the key item was the undesirability of presenting isolated
facts in botany texts, such as mentioning that peas are self-pollinated and
that peas were used by Mendel, without explaining why self-pollination was
essential to Mendel for carrying out his landmark experiments. There are far
too many isolated facts and names going about, when it would not be all that
much harder to teach concepts.
PvR

Dear David,

I note you feel you are occupied "just pointing out [my] errors".
Although I would readily admit any errors I might have made it would seem I
cannot see you actually pointing out any. If I have to describe what it is
you are doing it would seem you fasten upon I word I use, you connect this
with a
random word you derive from an unknown source and off you go ...

Since you were kind enough to provide such a clear example I will use that
to set the record straight. I stated:
"It is like expressing human progress over the last millenia by measuring
individual body weight: this may be be useful data but presents only a small
part of the picture".
If one were to conduct a poll as to what constitutes "human progress over
the last millenia" one might get quite different answers, such as the
invention of the wheel, the agricultural revolution, the invention of the
printing press, the industrial revolution, instant coffee, automobiles,
computers, cell-phones, nintendo, etc but genetic change would not be high
on the list, perhaps not even in the top thousand.
Yet you blithely state "Measuring a change in allele frequency is not at all
like "measuring individual body weight" as you suggest. Human body weight is
largely a function of environment, not genetics."

Although I am sure you will take this the wrong way, I feel honor bound to
advise you, with all due respect, to confer with your doctor about your
medication.

As to gene expression it is clear you are hampered by some severe
misconceptions. The safe advice would be for you to refrain from commenting
on this topic. This is the more so since it would not be enough for you to
read a book on the topic. As I am sure you are aware re-education is much
harder than education. You would need to take a course on the topic to
straighten matters out, and this might come hard. You had better avoid it.
Sorry to be so blunt.

sincerely,
PvR

The human genome project has shown that some human genes originated in
bacteria and have been passed to humans from the bacteria by horizontal
transfer.

There is no reason to believe that this is unique to humans and has almost
certainly happened to many other organisms in other kingdoms as well as
humans.

This is evolutionary, but does not involve the mutation of any alleles,
merely the addition of new (for that organism) alleles.

I am not, of course, saying that mutations do not happen, just that there
are other ways for the genome of any organism to change possibly leading to
selection and thus evolution.

John

"Don't ask me what I think of you, I might not give the answer you want me
to, Oh well." - Peter Green

"David Hershey" wrote in message
om...
If chance mutations don't give rise to new alleles in plant species,
then how do they arise? Many alleles do not code for "normal" or
functional proteins. The explanation is that the abnormal alleles
arose via mutations in the existing normal allele.

snip

I often cite references to support my scientific facts. You are the
one who almost always relies on an "unknown source" and will not
reveal your sources even when asked.

You are the one who has gone off on many tangents in this thread, e.g.
talking about human genetics and human body weight that have nothing
to do with botany. I am just responding to topics that you have
brought up such as your homozygous versus heterozygous disease
susceptibility hypothesis.

I have pointed out many of your errors, e.g.

1. Your incorrect generalization that a homozygous crop will be more
disease susceptible than a heterozygous crop.

2. Your harsh criticism of the definition of evolution I quoted, i.e.
"...evolution can be precisely defined as any change in the frequency
of alleles within a gene pool from one generation to the next." You
are apparently unable to substantiate the criticisms or provide a more
accurate definition.

3. Your rejecting the concept that mutation plays an essential role in
evolution by stating "it is pretty clear that mutations as such are
not really the factor they were made out to be" but then countering
that "The present understanding of gene change can be briefly stated
as 'Cut, Copy, Paste.'" The "Cut, Copy, Paste" mechanism that results
in gene change is considered mutation:
http://users.rcn.com/jkimball.ma.ult...ansposons.html

Biology textbooks and websites agree that mutation plays an important
role in evolution. For example, a Tulane University evolution class
website notes that "the major role of mutation in evolution is the
introduction of new gene variants into a population":
http://www.tulane.edu/~eeob/Courses/...ng_sp2000.html

4. Your contention that "extra genes/alleles have additional effects"
contradicts your favorite plant example that Coffea arabica with 44
chromosomes is more disease susceptible than C. canephora with just
22, yet you will not even address the discrepancy when asked.

I took college courses in biology, botany, plant breeding and genetics
and have read a lot on evolution, including college biology and botany
textbooks, science teaching journals like American Biology Teacher,
noncreationist evolution websites, and the U.S. National Academy of
Science's book, Teaching About Evolution and the Nature of Science
(1998) which can be read online for free:
http://www.nap.edu/books/0309063647/html/index.html

The 1994 college biology text by John Kimball is available online for
free and I find it a good introductory source for evolution and
biology information:
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/

Many other college botany and biology textbooks have websites that
provide some free information, e.g.
Biology of Plants by Raven, Evert and Eichorn:
http://www.whfreeman.com/raven/index.htm

What have been your sources of information on evolution and plant
biology?

Any reasonable person can see that your personal attacks on me
indicate that you have no scientific facts or arguments to back your
claims. If science was on your side, it would be very easy for you to
support your case with facts from books or websites.

David R. Hershey



"P van Rijckevorsel" wrote in message ...
Dear David,

I note you feel you are occupied "just pointing out [my] errors".
Although I would readily admit any errors I might have made it would seem I
cannot see you actually pointing out any. If I have to describe what it is
you are doing it would seem you fasten upon I word I use, you connect this
with a
random word you derive from an unknown source and off you go ...

Since you were kind enough to provide such a clear example I will use that
to set the record straight. I stated:
"It is like expressing human progress over the last millenia by measuring
individual body weight: this may be be useful data but presents only a small
part of the picture".
If one were to conduct a poll as to what constitutes "human progress over
the last millenia" one might get quite different answers, such as the
invention of the wheel, the agricultural revolution, the invention of the
printing press, the industrial revolution, instant coffee, automobiles,
computers, cell-phones, nintendo, etc but genetic change would not be high
on the list, perhaps not even in the top thousand.
Yet you blithely state "Measuring a change in allele frequency is not at all
like "measuring individual body weight" as you suggest. Human body weight is
largely a function of environment, not genetics."

Although I am sure you will take this the wrong way, I feel honor bound to
advise you, with all due respect, to confer with your doctor about your
medication.

As to gene expression it is clear you are hampered by some severe
misconceptions. The safe advice would be for you to refrain from commenting
on this topic. This is the more so since it would not be enough for you to
read a book on the topic. As I am sure you are aware re-education is much
harder than education. You would need to take a course on the topic to
straighten matters out, and this might come hard. You had better avoid it.
Sorry to be so blunt.

sincerely,
PvR

I agree that mutation is not the only source of variation that can
lead to evolution but it certainly is a very important source. Even in
your example of horizontal gene flow from bacteria to humans, it is
likely that some of those genes and alleles arose via mutation prior
to the horizontal transfer. The leading proponent of horizontal
transfer, Carl Woese of the University of Illinois, believes that
three cell types, bacteria, eukaryote and archaea, arose independently
and underwent a lot of horizontal transfers early in evolution:
http://www.usatoday.com/news/healths...-evolution.htm

Even with three independent origins of cells, there would have been
little genetic variation to begin with. Thus, wouldn't the greater
part of the huge number of genes and alleles present today have arisen
by mutation over the 3-4 billion years after the origin of life?

David R. Hershey



"John Margetts" wrote in message ...
The human genome project has shown that some human genes originated in
bacteria and have been passed to humans from the bacteria by horizontal
transfer.

There is no reason to believe that this is unique to humans and has almost
certainly happened to many other organisms in other kingdoms as well as
humans.

This is evolutionary, but does not involve the mutation of any alleles,
merely the addition of new (for that organism) alleles.

I am not, of course, saying that mutations do not happen, just that there
are other ways for the genome of any organism to change possibly leading to
selection and thus evolution.

John

"Don't ask me what I think of you, I might not give the answer you want me
to, Oh well." - Peter Green

"David Hershey" wrote in message
om...
If chance mutations don't give rise to new alleles in plant species,
then how do they arise? Many alleles do not code for "normal" or
functional proteins. The explanation is that the abnormal alleles
arose via mutations in the existing normal allele.

snip