| Topic: |
Religions > Atheism |
| User: |
"david ford" |
| Date: |
28 Feb 2005 02:22:42 PM |
| Object: |
Re: The Misrepresentations of Richard Forrest |
Larry Moran wrote:
On 22 Feb 2005 Seanpit <seanpitnospam@naturalselection.0catch.com> wrote:
Paul J Gans,
I don't have much time today to respond to nonsense, but this was just
too hilarious to pass up. You wrote:
[*] Could you please stop with this "amino acid" crap? There
are NO amino acids present in a protein. There are entities
that could be amino acids if they existed freely.
Oh really?! What do you call the individual molecules that "used to be
amino acids" when they are linked together in a peptide chain? Hint:
amino acids.
I call them *amino acid residues* or just plain *residues* and so do
most
other biochemists.
What approximate percentage of
1) biologists, and
2) biochemists,
use "amino acids" in their verbal and e-mail conversations?
You earlier recommended that IDiots not be debated, but rather laughed
at. Are you now changing your recommendation?
Ref:
http://groups.google.co.in/groups?selm=dford3-37pdfuF5cvmh7U1%40individual.net
Amino Acid/Protein Definitions: "The fundamental building blocks of a
protein molecule. A protein is composed of a chain of hundreds or
thousands of amino acids. . . In proteins, amino acids are joined
together when the NH2 group of one forms a bond with the COOH group of
the adjacent amino acid. The side group is what distinguishes each of
the amino acids from the others. . . Amino acids join together and form
short chains (peptides) or much longer chains (polypeptides). Over 80
amino acids are known to occur naturally, with 20 found commonly in
protein polypeptides."
http://www.google.com/search?hl=en&lr=&oi=defmore&q=define:Amino+Acid
Coincidently, I'm currently involved in a discussion with my students
about
the uses of the internet. The bottom line is that real biochemistry
textbooks,
and biochemistry professors, are much more reliable sources of
information
than web pages. Google gets you crap.
[LM]"biochemistry textbooks... are much more reliable sources of
information than web pages"
Shapiro, Robert. _Origins: A Skeptic's Guide to the Creation
of Life on Earth_ (GB: Penguin Books, 1986), 332pp.
On 108:
Confusion also exists concerning the actual products of
the experiments. Miller has certainly been forthright
and accurate in his publications and summaries. Yet we
find the following statement in A. L. Lehninger's widely
used textbook, _Biochemistry_: "Many different forms
of energy or radiation lead to organic compounds from
such simple gas mixtures, including representatives of
all the important types of molecules found in cells as
well as many not found in cells." That statement, as
written, is simply incorrect. For some molecules it is
true, if one ignores considerations of yield and attributes
significance to the mere presence of a substance, in
whatever amount. Recently, for example, Cyril
Ponnamperuma detected the five bases used in DNA and
RNA (which contain from twelve to sixteen atoms each)
in both a Miller-Urey type of mixture and a meteorite.
The compounds occurred to the extent of perhaps 2 parts
per million, yet Ponnamperuma in a news conference a
called it "almost an awesome result." The awe must lie in
the eye of the beholder. Nothing within the result
compels it.
Other biochemical substances, nucleosides for example,
have never been reported in any amount in such sources,
yet a mythology has emerged that maintains the
opposite, and extends this conclusion to even more
complicated molecules. I have seen several statements
in scientific sources which claim that proteins and
nucleic acids themselves have been prepared by
subjecting a reducing atmosphere to various energy
sources. These errors reflect the operation of an entire
belief system, one that I call predestinist.
Compare Scott in
1985 A.G. Cairns-Smith, 1986 Andrew Scott, 1999 Freeman Dyson
http://groups.google.co.in/groups?selm=dford3-33bltcF3rgbovU1%40individual.net
I've told my students that if they rely on the world wide web for their
information they might be given a failing grade.
Even if it's from the website http://www.talkorigins.org ?
Where on the web can I read "Laurence Moran's Evolution Home Page"?
[LM]"Google gets you crap." I did a Google search for:
Laurence Moran evolution
Are these Google-found webpages [LM]"crap"?:
http://www.talkorigins.org/faqs/evolution-definition.html
http://www.talkorigins.org/faqs/evolution-fact.html
http://www.biology.ualberta.ca/courses.hp/biol321/biol321.htm
http://www.skepticfiles.org/origins/evoludef.htm
When these entities are bonded together in a protein they
cease being amino acids.
LOL - too funny! See if some of your buddies in this forum will agree
with you on this one.
I agree with Paul. Here's what I wrote in my book.
"The linkage formed between amino acids is a secondary amide bond
called a peptide bond (Figure 3.9). This linkage can be thought of
as resulting from a simple condensation of the alpha-carboxyl group
of one amino acid with the alpha-amino group of another. Note
that a
water molecule is lost from the condensing amino acids in the
reaction.
(Recall from Section 2.6 that such simple condensation reactions
are
extremely unfavorable in aqueous solutions due to the huge
excess of
water molecules.
Let me guess: you consequently don't think spontaneous generation
occurred in a primordial soup. Did I get that right?
And besides, there was no primordial soup.
Ref:
fabled primordial soup never existed
http://groups.google.co.in/groups?selm=dford3-37mt00F5fb7kmU1%40individual.net
What spontaneous generation scenario does the textbook you wrote
endorse, if any?
Suppose you became an IDiot regarding the origin of the first biological
lifeform, and that change became well-known.
Would that change in your views impact sales of your textbook, and, if
so how?
Would you be asked to leave your university job? I'm thinking about
what happened to Steele and one IDiot.
http://groups.google.co.in/groups?selm=dford3-37pdfuF5cvmh7U1%40individual.net
Would you be stripped of your right to teach biochemistry courses?
(While a "tenured professor at San Francisco State University in the
early 1980s, Kenyon faced hearings and was stripped of the
right to teach biology courses because he criticized some aspects of
neo-Darwinian theory." Ref in
1984 Dean Kenyon
http://groups.google.co.in/groups?selm=dford3-34j9b2F4a5gioU1%40individual.net
The actual pathway of protein synthesis involves
reactive intermediates that overcome this limitation.)
The products of mind/intelligence, including the workproduct known as
the first biological lifeform, can do things that physics alone cannot do.
I've appealed to various lines of evidence in charging that the
worldview philosophy of materialism goes against reality.
Ref:
Reality vs. worldview philosophy of materialism
http://groups.google.co.in/groups?selm=dford3-3813ksF5ggkc3U1%40individual.net
Are you going to respond to my charge?
Or are you going to leave my remarks unchallenged?
Unlike the
carboxyl and amino groups of free amino acids in solution, the
groups
involved in peptide bonds carry no ionic charges.
Linked amino acid moieties in a polypeptide chain are called amino
acid residues. The names of residues are formed by replacing the
ending -ine or -ate with -yl. For example, a glycine residue in a
polypeptide is called glycyl, and a glutamate residue is called
glutamyl. In the cases of asparagine, glutamine, and cysteine, -yl
replaces the final -e to form asparaginyl, glutaminyl, and
cysteinyl,
respectively. The -yl ending indicates that the residue is an acyl
unit (a structure that lacks the hydroxyl of the carboxyl
group). The
dipeptide in Figure 3.9 is called alanylserine because alanine is
converted to an acyl unit but the amino acid serine retains its
carboxyl group.
The free amino group and free carboxyl group at the opposite
ends of
a peptide chain are called the N-terminus (amino terminus) and the
C-terminus (carboxyl terminus), respectively. At neutral pH, each
terminus carries an ionic charge. By convention, amino acid
residues
in a peptide chain are numbered from the N-terminus to the
C-terminus
and are usually written from left to right. This convention
corresponds
to the direction of protein synthesis (Section 22.6). Synthesis
begins
with the N-terminal amino acid - almost always methionine (Section
22.5) - and proceeds sequentially toward the C-terminus by
adding one
residue at a time.
Thus when you talk about the action of 1000 amino acids, anybody
with any actual knowlege thinks of a beaker with 1000 different
amino acids in it.
I'm obviously talking about peptide chains (single or multiple) with
specified arrangements of amino acids. I'm not sure how you can be
such a numbskull?! But, it is entertaining ; )
Of course we know that is not what you mean. But by using
incorrect (and obfuscatory language) you give yourself wiggle
room.
Go to any biochemistry textbook and see if they do not use the same
"obfuscatory" language to describe polypeptides/proteins made up of
chains of "amino acids". Where did you get this nonsense?
He may have gotten it (I hope) from my biochemistry textbook. :-)
On the other hand, he may have gotten it from the Voet & Voet
Biochemistry
textbook (3rd edition) because they also refer to *amino acid residues*
and not to free amino acids.
"Proteins are molecules that consist of one or more polypeptide
chains. These polypeptides range in length from ~40 to ~33,000
amino acid residues (although few have more than 1500 residues)
and, since the average mas of an amino acid residue is ~110 D,
have molecular masses that range from ~4 to over ~3600 kD."
.... page 68
But who knows? Paul could also have read the latest edition (5th) of
Berg, Tymoczko, and Stryer ..
"A series of amino acids joined by peptide bonds form a polypeptide
chain, and each amino acid in a polypeptide is called a residue."
.... page 51
Let's not forget those crazy people at Worth Publishers. Their offices
are on Madison Avenue in New York City and that's only a short subway
ride from where Paul Gans hangs out. I suppose it's possible that he
read Lehninger Principles of Biochemistry insead of my book. (Boo!)
[LM]"Boo!" indeed.
"Proteins are dehydration polymers of amino acids, with each
*amino acid residue* joined to its neighbor by a specific type
of covalent bond. (The term "residue" reflects the loss of the
elements of water when one amino acid is joined to another.)
.... page 116
None of this adds to your credibility.
Especially with those who don't know what the heck they are talking
about.
Count me among those who don't know what I'm talking about. At least I'm
in good company.
Would you give any of these Larry Moran remarks [LM]"a failing grade,"
and if so, which ones?:
LM in
http://groups.google.co.in/groups?selm=7br95q%24efv%241%40bioinfo.med.utoronto.ca
Maybe you could write a paragraph or two describing
to students how the protein folding problem was solved
and how you envisage the formation of a well defined
three dimensional structure from a linear chain of amino
acids.
LM in
http://groups.google.co.in/groups?selm=8p67cq%24gg1%241%40bioinfo.med.utoronto.ca
In general, many species will have a different amino
acid sequence and within species there will be variants.
LM in
http://groups.google.co.in/groups?selm=8q7p14%24h1h%241%40bioinfo.med.utoronto.ca
I've extracted the human (top) and E. coli (bottom)
sequences to show the alignment. Asterisks indicate
identical amino acids.
LM in
http://groups.google.co.in/groups?selm=702lqf%24rbm%241%40bioinfo.med.utoronto.ca
Lactate dehydrogenase and malate dehydrogenase are
related proteins that are only 28% identical in amino
acid sequence.
LM in
http://groups.google.co.in/groups?selm=8j08js%24ebk%241%40bioinfo.med.utoronto.ca
But if you think DsbA and thioredoxin are homologous
then you must be assuming that there have been lots of
changes in the structures of these two proteins. Right?
Have you thought about how you can get from one to
the other by substituting all of the amino acids, losing
most of the structure, but preserving a small beta sheet?
LM in
http://groups.google.co.in/groups?selm=aghv5l%248po%241%40bioinfo.med.utoronto.ca
What it means is that the rattlesnake amino acid
sequence does not fit into the phylogenetic tree at a
place where we would expect it.
Would you give any of these Gould remarks [LM]"a failing grade," and if
so, which ones?:
Luria, Salvador E., Stephen Jay Gould, and Sam Singer.
1981. _A View of Life_ (USA: The Benjamin/Cummings
Publishing Company, Inc.), 806pp. On 55, 57:
Only 20 different amino acids (of the 100 or more that
exist) take part in making up the polypeptide chains of
all proteins. .... The sequence of amino acids in a
polypeptide is called its primary structure. Even though
all proteins consist of unbranched chains of amino acids,
most proteins do not exist as long straight chains....
Some similar Dawkins remarks were referenced in
http://groups.google.co.in/groups?selm=dford3-386md9F5lsv5cU1%40individual.net
.
|
|
| User: "Glenn" |
|
| Title: Re: The Misrepresentations of Richard Forrest |
02 Mar 2005 01:30:06 AM |
|
|
"david ford" <dford3@gl.umbc.edu> wrote in message
news:dford3-38hcs9F5ovk6pU1@individual.net...
Larry Moran wrote:
On 22 Feb 2005 Seanpit <seanpitnospam@naturalselection.0catch.com>
wrote:
Paul J Gans,
I don't have much time today to respond to nonsense, but this was just
too hilarious to pass up. You wrote:
[*] Could you please stop with this "amino acid" crap? There
are NO amino acids present in a protein. There are entities
that could be amino acids if they existed freely.
Oh really?! What do you call the individual molecules that "used to be
amino acids" when they are linked together in a peptide chain? Hint:
amino acids.
I call them *amino acid residues* or just plain *residues* and so do
most
other biochemists.
What approximate percentage of
1) biologists, and
2) biochemists,
use "amino acids" in their verbal and e-mail conversations?
You earlier recommended that IDiots not be debated, but rather laughed
at. Are you now changing your recommendation?
Ref:
http://groups.google.co.in/groups?selm=dford3-37pdfuF5cvmh7U1%40individual.net
Amino Acid/Protein Definitions: "The fundamental building blocks of a
protein molecule. A protein is composed of a chain of hundreds or
thousands of amino acids. . . In proteins, amino acids are joined
together when the NH2 group of one forms a bond with the COOH group of
the adjacent amino acid. The side group is what distinguishes each of
the amino acids from the others. . . Amino acids join together and form
short chains (peptides) or much longer chains (polypeptides). Over 80
amino acids are known to occur naturally, with 20 found commonly in
protein polypeptides."
http://www.google.com/search?hl=en&lr=&oi=defmore&q=define:Amino+Acid
Coincidently, I'm currently involved in a discussion with my students
about
the uses of the internet. The bottom line is that real biochemistry
textbooks,
and biochemistry professors, are much more reliable sources of
information
than web pages. Google gets you crap.
[LM]"biochemistry textbooks... are much more reliable sources of
information than web pages"
Shapiro, Robert. _Origins: A Skeptic's Guide to the Creation
of Life on Earth_ (GB: Penguin Books, 1986), 332pp.
On 108:
Confusion also exists concerning the actual products of
the experiments. Miller has certainly been forthright
and accurate in his publications and summaries. Yet we
find the following statement in A. L. Lehninger's widely
used textbook, _Biochemistry_: "Many different forms
of energy or radiation lead to organic compounds from
such simple gas mixtures, including representatives of
all the important types of molecules found in cells as
well as many not found in cells." That statement, as
written, is simply incorrect. For some molecules it is
true, if one ignores considerations of yield and attributes
significance to the mere presence of a substance, in
whatever amount. Recently, for example, Cyril
Ponnamperuma detected the five bases used in DNA and
RNA (which contain from twelve to sixteen atoms each)
in both a Miller-Urey type of mixture and a meteorite.
The compounds occurred to the extent of perhaps 2 parts
per million, yet Ponnamperuma in a news conference a
called it "almost an awesome result." The awe must lie in
the eye of the beholder. Nothing within the result
compels it.
Other biochemical substances, nucleosides for example,
have never been reported in any amount in such sources,
yet a mythology has emerged that maintains the
opposite, and extends this conclusion to even more
complicated molecules. I have seen several statements
in scientific sources which claim that proteins and
nucleic acids themselves have been prepared by
subjecting a reducing atmosphere to various energy
sources. These errors reflect the operation of an entire
belief system, one that I call predestinist.
Compare Scott in
1985 A.G. Cairns-Smith, 1986 Andrew Scott, 1999 Freeman Dyson
http://groups.google.co.in/groups?selm=dford3-33bltcF3rgbovU1%40individual.net
I've told my students that if they rely on the world wide web for their
information they might be given a failing grade.
Even if it's from the website http://www.talkorigins.org ?
Where on the web can I read "Laurence Moran's Evolution Home Page"?
LOL! It appears he took it down. Two links from other sites didn't work.
[LM]"Google gets you crap." I did a Google search for:
Laurence Moran evolution
Are these Google-found webpages [LM]"crap"?:
http://www.talkorigins.org/faqs/evolution-definition.html
http://www.talkorigins.org/faqs/evolution-fact.html
http://www.biology.ualberta.ca/courses.hp/biol321/biol321.htm
http://www.skepticfiles.org/origins/evoludef.htm
When these entities are bonded together in a protein they
cease being amino acids.
LOL - too funny! See if some of your buddies in this forum will agree
with you on this one.
I agree with Paul. Here's what I wrote in my book.
"The linkage formed between amino acids is a secondary amide bond
called a peptide bond (Figure 3.9). This linkage can be thought of
as resulting from a simple condensation of the alpha-carboxyl
group
of one amino acid with the alpha-amino group of another. Note
that a
water molecule is lost from the condensing amino acids in the
reaction.
(Recall from Section 2.6 that such simple condensation reactions
are
extremely unfavorable in aqueous solutions due to the huge
excess of
water molecules.
Let me guess: you consequently don't think spontaneous generation
occurred in a primordial soup. Did I get that right?
And besides, there was no primordial soup.
Ref:
fabled primordial soup never existed
http://groups.google.co.in/groups?selm=dford3-37mt00F5fb7kmU1%40individual.net
What spontaneous generation scenario does the textbook you wrote
endorse, if any?
Suppose you became an IDiot regarding the origin of the first biological
lifeform, and that change became well-known.
Would that change in your views impact sales of your textbook, and, if
so how?
Would you be asked to leave your university job? I'm thinking about
what happened to Steele and one IDiot.
http://groups.google.co.in/groups?selm=dford3-37pdfuF5cvmh7U1%40individual.net
Would you be stripped of your right to teach biochemistry courses?
(While a "tenured professor at San Francisco State University in the
early 1980s, Kenyon faced hearings and was stripped of the
right to teach biology courses because he criticized some aspects of
neo-Darwinian theory." Ref in
1984 Dean Kenyon
http://groups.google.co.in/groups?selm=dford3-34j9b2F4a5gioU1%40individual.net
The actual pathway of protein synthesis involves
reactive intermediates that overcome this limitation.)
The products of mind/intelligence, including the workproduct known as
the first biological lifeform, can do things that physics alone cannot do.
I've appealed to various lines of evidence in charging that the
worldview philosophy of materialism goes against reality.
Ref:
Reality vs. worldview philosophy of materialism
http://groups.google.co.in/groups?selm=dford3-3813ksF5ggkc3U1%40individual.net
Are you going to respond to my charge?
Or are you going to leave my remarks unchallenged?
Unlike the
carboxyl and amino groups of free amino acids in solution, the
groups
involved in peptide bonds carry no ionic charges.
Linked amino acid moieties in a polypeptide chain are called amino
acid residues. The names of residues are formed by replacing the
ending -ine or -ate with -yl. For example, a glycine residue in a
polypeptide is called glycyl, and a glutamate residue is called
glutamyl. In the cases of asparagine, glutamine, and cysteine, -yl
replaces the final -e to form asparaginyl, glutaminyl, and
cysteinyl,
respectively. The -yl ending indicates that the residue is an acyl
unit (a structure that lacks the hydroxyl of the carboxyl
group). The
dipeptide in Figure 3.9 is called alanylserine because alanine is
converted to an acyl unit but the amino acid serine retains its
carboxyl group.
The free amino group and free carboxyl group at the opposite
ends of
a peptide chain are called the N-terminus (amino terminus) and the
C-terminus (carboxyl terminus), respectively. At neutral pH, each
terminus carries an ionic charge. By convention, amino acid
residues
in a peptide chain are numbered from the N-terminus to the
C-terminus
and are usually written from left to right. This convention
corresponds
to the direction of protein synthesis (Section 22.6). Synthesis
begins
with the N-terminal amino acid - almost always methionine (Section
22.5) - and proceeds sequentially toward the C-terminus by
adding one
residue at a time.
Thus when you talk about the action of 1000 amino acids, anybody
with any actual knowlege thinks of a beaker with 1000 different
amino acids in it.
I'm obviously talking about peptide chains (single or multiple) with
specified arrangements of amino acids. I'm not sure how you can be
such a numbskull?! But, it is entertaining ; )
Of course we know that is not what you mean. But by using
incorrect (and obfuscatory language) you give yourself wiggle
room.
Go to any biochemistry textbook and see if they do not use the same
"obfuscatory" language to describe polypeptides/proteins made up of
chains of "amino acids". Where did you get this nonsense?
He may have gotten it (I hope) from my biochemistry textbook. :-)
On the other hand, he may have gotten it from the Voet & Voet
Biochemistry
textbook (3rd edition) because they also refer to *amino acid residues*
and not to free amino acids.
"Proteins are molecules that consist of one or more polypeptide
chains. These polypeptides range in length from ~40 to ~33,000
amino acid residues (although few have more than 1500 residues)
and, since the average mas of an amino acid residue is ~110 D,
have molecular masses that range from ~4 to over ~3600 kD."
.... page 68
But who knows? Paul could also have read the latest edition (5th) of
Berg, Tymoczko, and Stryer ..
"A series of amino acids joined by peptide bonds form a polypeptide
chain, and each amino acid in a polypeptide is called a residue."
.... page 51
Let's not forget those crazy people at Worth Publishers. Their offices
are on Madison Avenue in New York City and that's only a short subway
ride from where Paul Gans hangs out. I suppose it's possible that he
read Lehninger Principles of Biochemistry insead of my book. (Boo!)
[LM]"Boo!" indeed.
"Proteins are dehydration polymers of amino acids, with each
*amino acid residue* joined to its neighbor by a specific type
of covalent bond. (The term "residue" reflects the loss of the
elements of water when one amino acid is joined to another.)
.... page 116
None of this adds to your credibility.
Especially with those who don't know what the heck they are talking
about.
Count me among those who don't know what I'm talking about. At least
I'm
in good company.
Would you give any of these Larry Moran remarks [LM]"a failing grade,"
and if so, which ones?:
LM in
http://groups.google.co.in/groups?selm=7br95q%24efv%241%40bioinfo.med.utoronto.ca
Maybe you could write a paragraph or two describing
to students how the protein folding problem was solved
and how you envisage the formation of a well defined
three dimensional structure from a linear chain of amino
acids.
LM in
http://groups.google.co.in/groups?selm=8p67cq%24gg1%241%40bioinfo.med.utoronto.ca
In general, many species will have a different amino
acid sequence and within species there will be variants.
LM in
http://groups.google.co.in/groups?selm=8q7p14%24h1h%241%40bioinfo.med.utoronto.ca
I've extracted the human (top) and E. coli (bottom)
sequences to show the alignment. Asterisks indicate
identical amino acids.
LM in
http://groups.google.co.in/groups?selm=702lqf%24rbm%241%40bioinfo.med.utoronto.ca
Lactate dehydrogenase and malate dehydrogenase are
related proteins that are only 28% identical in amino
acid sequence.
LM in
http://groups.google.co.in/groups?selm=8j08js%24ebk%241%40bioinfo.med.utoronto.ca
But if you think DsbA and thioredoxin are homologous
then you must be assuming that there have been lots of
changes in the structures of these two proteins. Right?
Have you thought about how you can get from one to
the other by substituting all of the amino acids, losing
most of the structure, but preserving a small beta sheet?
LM in
http://groups.google.co.in/groups?selm=aghv5l%248po%241%40bioinfo.med.utoronto.ca
What it means is that the rattlesnake amino acid
sequence does not fit into the phylogenetic tree at a
place where we would expect it.
Would you give any of these Gould remarks [LM]"a failing grade," and if
so, which ones?:
Luria, Salvador E., Stephen Jay Gould, and Sam Singer.
1981. _A View of Life_ (USA: The Benjamin/Cummings
Publishing Company, Inc.), 806pp. On 55, 57:
Only 20 different amino acids (of the 100 or more that
exist) take part in making up the polypeptide chains of
all proteins. .... The sequence of amino acids in a
polypeptide is called its primary structure. Even though
all proteins consist of unbranched chains of amino acids,
most proteins do not exist as long straight chains....
Some similar Dawkins remarks were referenced in
http://groups.google.co.in/groups?selm=dford3-386md9F5lsv5cU1%40individual.net
.
|
|
|
|
| User: "Tracy Hamilton" |
|
| Title: Re: The Misrepresentations of Richard Forrest |
28 Feb 2005 06:28:49 PM |
|
|
"david ford" <dford3@gl.umbc.edu> wrote in message
news:dford3-38hcs9F5ovk6pU1@individual.net...
Larry Moran wrote:
On 22 Feb 2005 Seanpit <seanpitnospam@naturalselection.0catch.com>
wrote:
Paul J Gans,
I don't have much time today to respond to nonsense, but this was just
too hilarious to pass up. You wrote:
[*] Could you please stop with this "amino acid" crap? There
are NO amino acids present in a protein. There are entities
that could be amino acids if they existed freely.
Oh really?! What do you call the individual molecules that "used to be
amino acids" when they are linked together in a peptide chain? Hint:
amino acids.
I call them *amino acid residues* or just plain *residues* and so do
most
other biochemists.
What approximate percentage of
1) biologists, and
2) biochemists,
use "amino acids" in their verbal and e-mail conversations?
4 out of 5 biochemists. The fifth is temporarily dazed from
trying to make sense of the muddle that is Sean Pitman's
proposals.
[snip]
Amino Acid/Protein Definitions: "The fundamental building blocks of a
protein molecule. A protein is composed of a chain of hundreds or
thousands of amino acids. . . In proteins, amino acids are joined
together when the NH2 group of one forms a bond with the COOH group of
the adjacent amino acid. The side group is what distinguishes each of
the amino acids from the others. . . Amino acids join together and form
short chains (peptides) or much longer chains (polypeptides). Over 80
amino acids are known to occur naturally, with 20 found commonly in
protein polypeptides."
http://www.google.com/search?hl=en&lr=&oi=defmore&q=define:Amino+Acid
Coincidently, I'm currently involved in a discussion with my students
about
the uses of the internet. The bottom line is that real biochemistry
textbooks,
and biochemistry professors, are much more reliable sources of
information
than web pages. Google gets you crap.
[LM]"biochemistry textbooks... are much more reliable sources of
information than web pages"
Shapiro, Robert. _Origins: A Skeptic's Guide to the Creation
of Life on Earth_ (GB: Penguin Books, 1986), 332pp.
On 108:
[snip - nothing about using residues vs amino acids for proper terminology,
nor from a biochemistry text, nor from even a recent biochemistry
text]
I've told my students that if they rely on the world wide web for their
information they might be given a failing grade.
Even if it's from the website http://www.talkorigins.org ?
Where on the web can I read "Laurence Moran's Evolution Home Page"?
If that is all a student writing a report on evolution cites for explaining
it,
he had damn well get an F! Why do you think there are references on
talk.origins? For people to ignore? Note that these are to biology
textbooks, just like
he was referring anybody wanting to know the proper terminology in
biochemistry he used biochemistry textbooks.
You are not very good at this - give it up!
[LM]"Google gets you crap." I did a Google search for:
Laurence Moran evolution
Are these Google-found webpages [LM]"crap"?:
http://www.talkorigins.org/faqs/evolution-definition.html
No. But I can tell you a guaranteed way to get crap. Do a google
groups search for author Ford, David. Actually, we don't need to do this,
do we? You do it often enough for us.
[snip inanity]
Would you give any of these Larry Moran remarks [LM]"a failing grade,"
and if so, which ones?:
LM in
http://groups.google.co.in/groups?selm=7br95q%24efv%241%40bioinfo.med.utoronto.ca
Maybe you could write a paragraph or two describing
to students how the protein folding problem was solved
and how you envisage the formation of a well defined
three dimensional structure from a linear chain of amino
acids.
It sounds like a good question to me. What do you know about the
protein folding problem? Apparently - NOTHING!
[further snippage - it is more of the same level, or worse]
Tracy P. Hamilton
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| User: "Pithecanthropus Erectus" |
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| Title: Proteome Folding (was) Re: The Misrepresentations of Richard Forrest |
01 Mar 2005 01:20:44 PM |
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It sounds like a good question to me. What do you know about the
protein folding problem? Apparently - NOTHING!
[further snippage - it is more of the same level, or worse]
Tracy P. Hamilton
If any of you would like to do something useful with your computers (I
mean besides porn,) you can participate in the world community grid's
project on proteome folding. I am participating, so that when the
processing is all done, people will think that I actually know what the
hell it means.
http://www.worldcommunitygrid.org
http://www.worldcommunitygrid.org/stat/global.html
I was donating my processor for Setiathome, but dedcided that this is a
little more down to earth.
http://www.worldcommunitygrid.org/stat/proteome.html
Mike
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| User: "Tracy Hamilton" |
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| Title: Re: Proteome Folding (was) Re: The Misrepresentations of Richard Forrest |
01 Mar 2005 04:52:40 PM |
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"Pithecanthropus Erectus" <tuibguy1EGNUM@comcast.net> wrote in message
news:zeKdncQNcLEMXbnfRVn-2Q@comcast.com...
It sounds like a good question to me. What do you know about the
protein folding problem? Apparently - NOTHING!
[further snippage - it is more of the same level, or worse]
Tracy P. Hamilton
If any of you would like to do something useful with your computers (I
mean besides porn,) you can participate in the world community grid's
project on proteome folding. I am participating, so that when the
processing is all done, people will think that I actually know what the
hell it means.
Perhaps. The most successful approaches are heavily dependent on
searching stretches of primary sequence in the "unknown" protein
for similar patterns with known folds, guessing secondary
structure and proceeding from there.
That gives around 70% success for proteins in water solution and
40% for membrane proteins, at least in the latest protein
structure prediction competition (CASP6).
For a graphical picture of the results go to
http://predictioncenter2.llnl.gov/casp/casp6/public/cgi-bin/results.cgi
The x axis is percent of residues correctly predicted within the
distance given on the y axis. Therefore what I would consider a success is
a
graph that does not go above five angstroms, period. Look at the graph for
T0216. The best was to get 10% of residue-residue distances within
the cutoff (which I could not find).
Tracy P. Hamilton
http://www.worldcommunitygrid.org
http://www.worldcommunitygrid.org/stat/global.html
I was donating my processor for Setiathome, but dedcided that this is a
little more down to earth.
http://www.worldcommunitygrid.org/stat/proteome.html
Mike
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| User: "Bobby D. Bryant" |
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| Title: Re: Proteome Folding (was) Re: The Misrepresentations of Richard Forrest |
01 Mar 2005 01:41:44 PM |
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On Tue, 01 Mar 2005, Pithecanthropus Erectus <tuibguy1EGNUM@comcast.net> wrote:
If any of you would like to do something useful with your computers (I
mean besides porn,) you can participate in the world community grid's
project on proteome folding.
I haden't even heard of the porn folding project.
--
Bobby Bryant
Austin, Texas
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| User: "" |
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| Title: Re: Proteome Folding (was) Re: The Misrepresentations of Richard Forrest |
01 Mar 2005 02:40:29 PM |
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Bobby D. Bryant wrote:
On Tue, 01 Mar 2005, Pithecanthropus Erectus
<tuibguy1EGNUM@comcast.net> wrote:
If any of you would like to do something useful with your computers
(I
mean besides porn,) you can participate in the world community
grid's
project on proteome folding.
I haden't even heard of the porn folding project.
I understand Hugh Hefner is the primary sponsor...
.
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| User: "John Wilkins" |
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| Title: Re: Proteome Folding (was) Re: The Misrepresentations of Richard Forrest |
01 Mar 2005 05:03:59 PM |
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<cubist@aol.com> wrote:
Bobby D. Bryant wrote:
On Tue, 01 Mar 2005, Pithecanthropus Erectus
<tuibguy1EGNUM@comcast.net> wrote:
If any of you would like to do something useful with your computers
(I
mean besides porn,) you can participate in the world community
grid's
project on proteome folding.
I haden't even heard of the porn folding project.
I understand Hugh Hefner is the primary sponsor...
It's easily solvable - all folds are Z folds
--
John S. Wilkins AA#2207
web: www.wilkins.id.au blog: evolvethought.blogspot.com
Fiat lunch!
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| User: "Paul J Gans" |
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| Title: Re: Proteome Folding (was) Re: The Misrepresentations of Richard Forrest |
01 Mar 2005 07:59:09 PM |
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In talk.origins wrote:
Bobby D. Bryant wrote:
On Tue, 01 Mar 2005, Pithecanthropus Erectus
<tuibguy1EGNUM@comcast.net> wrote:
If any of you would like to do something useful with your computers
(I
mean besides porn,) you can participate in the world community
grid's
project on proteome folding.
I haden't even heard of the porn folding project.
I understand Hugh Hefner is the primary sponsor...
I think he's folded.
---- Paul J. Gans
.
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| User: "Bobby D. Bryant" |
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| Title: Re: Proteome Folding (was) Re: The Misrepresentations of Richard Forrest |
01 Mar 2005 05:10:36 PM |
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On Tue, 01 Mar 2005, wrote:
Bobby D. Bryant wrote:
On Tue, 01 Mar 2005, Pithecanthropus Erectus
<tuibguy1EGNUM@comcast.net> wrote:
If any of you would like to do something useful with your computers (I
mean besides porn,) you can participate in the world community grid's
project on proteome folding.
I haden't even heard of the porn folding project.
I understand Hugh Hefner is the primary sponsor...
Ah, I had forgotten about the Sinner Fold.
--
Bobby Bryant
Austin, Texas
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| User: "david ford" |
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| Title: Re: The Misrepresentations of Richard Forrest |
02 Mar 2005 09:21:31 AM |
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Tracy Hamilton <DontSpamhamilton@uab.edu> on 28 Feb 2005:
david ford <dford3@gl.umbc.edu> wrote in message
news:dford3-38hcs9F5ovk6pU1@individual.net...
Larry Moran wrote:
On 22 Feb 2005 Seanpit
<seanpitnospam@naturalselection.0catch.com> wrote:
Paul J Gans,
I don't have much time today to respond to nonsense, but this was
just
too hilarious to pass up. You wrote:
[*] Could you please stop with this "amino acid" crap? There
are NO amino acids present in a protein. There are entities
that could be amino acids if they existed freely.
Oh really?! What do you call the individual molecules that "used
to be
amino acids" when they are linked together in a peptide chain? Hint:
amino acids.
I call them *amino acid residues* or just
plain *residues* and so do most
other biochemists.
What approximate percentage of
1) biologists, and
2) biochemists,
use "amino acids" in their verbal and e-mail conversations?
4 out of 5 biochemists. The fifth is temporarily dazed from
trying to make sense of the muddle that is Sean Pitman's
proposals.
I hope Larry doesn't stay [TH]"dazed" for long, since I
eagerly await new posts of his.
What approximate percentage of biologists use "amino acids" in their
verbal and e-mail conversations?
When Mathews & van Holde wrote of an
[M&vH]"amino acid sequence," did they use [TH]"proper
terminology"?:
Mathews, Christopher K. and K. E. van Holde. 1990.
_Biochemistry_ (USA: The Benjamin/Cummings Publishing
Co., Inc.), 1129pp. On 148:
Every protein has a defined order of amino acid
residues. As with the nucleic acids, this sequence is
referred to as the _primary structure_ of the protein.
Figure 5.14 shows the amino acid sequence of sperm
whale myoglobin, the protein whose structure we saw in
Figure 5.1.
[snip]
Amino Acid/Protein Definitions: "The fundamental building blocks of a
protein molecule. A protein is composed of a chain of hundreds or
thousands of amino acids. . . In proteins, amino acids are joined
together when the NH2 group of one forms a bond with the COOH
group of
the adjacent amino acid. The side group is what distinguishes each of
the amino acids from the others. . . Amino acids join together
and form
short chains (peptides) or much longer chains (polypeptides). Over 80
amino acids are known to occur naturally, with 20 found commonly in
protein polypeptides."
http://www.google.com/search?hl=en&lr=&oi=defmore&q=define:Amino+Acid
Coincidently, I'm currently involved in a discussion with my
students about the uses of the internet. The bottom line is
that real biochemistry textbooks, and biochemistry
professors, are much more reliable sources of
information than web pages. Google gets you crap.
[LM]"biochemistry textbooks... are much more reliable sources of
information than web pages"
Shapiro, Robert. _Origins: A Skeptic's Guide to the Creation
of Life on Earth_ (GB: Penguin Books, 1986), 332pp.
On 108:
[snip - nothing about using residues vs amino acids for proper
terminology,
nor from a biochemistry text, nor from even a recent biochemistry
text]
Before you snipped Shapiro, did you read it? Shapiro had
quoted [TH]"from a biochemistry text" and pointed out the
erroneousness of the claim that that biochemistry text made.
Compare [LM]"biochemistry textbooks... are much more reliable sources of
information than web pages"
BTW, Larry quoted from that same textbook in the post to which
I replied.
I've told my students that if they rely on the world wide web for
their
information they might be given a failing grade.
Even if it's from the website http://www.talkorigins.org ?
Where on the web can I read "Laurence Moran's Evolution Home Page"?
If that is all a student writing a report on evolution cites for
explaining
it,
he had damn well get an F! Why do you think there are references on
talk.origins? For people to ignore?
Please rephrase your question without using the word "why."
Note that these are to biology
textbooks, just like
he was referring anybody wanting to know the proper terminology in
biochemistry he used biochemistry textbooks.
You are not very good at this - give it up!
[LM]"Google gets you crap." I did a Google search for:
Laurence Moran evolution
Are these Google-found webpages [LM]"crap"?:
http://www.talkorigins.org/faqs/evolution-definition.html
No. But I can tell you a guaranteed way to get crap. Do a google
groups search for author Ford, David. Actually, we don't need to do
this,
do we? You do it often enough for us.
And you, Tracy, do a marvelous job of shooting it down.
What is your response to this post?:
Reality vs. worldview philosophy of materialism
http://groups.google.co.in/groups?selm=dford3-3813ksF5ggkc3U1%40individual.net
[snip inanity]
Would you give any of these Larry Moran remarks [LM]"a failing grade,"
and if so, which ones?:
LM in
http://groups.google.co.in/groups?selm=7br95q%24efv%241%40bioinfo.med.utoronto.ca
Maybe you could write a paragraph or two describing
to students how the protein folding problem was solved
and how you envisage the formation of a well defined
three dimensional structure from a linear chain of amino
acids.
It sounds like a good question to me. What do you know about the
protein folding problem? Apparently - NOTHING!
Nothing new there.
[further snippage - it is more of the same level, or worse]
In the Larry quotations you snipped, do you think Larry
used [TH]"proper terminology" with regards to
[TH]"using residues vs amino acids"?
You mentioned biology textbooks. Do you consider this
Alberts and its accompanying figure [LM]"reliable"?:
Alberts, Bruce, Dennis Bray, Julian Lewis, Martin Raff,
Keith Roberts, James D. Watson. 1983. _Molecular Biology
of the Cell_ (USA: Garland Publishing, Inc.), 1146 + 35pp.
On 825, a caption that accompanies a rendering of Haeckel's
fraudulent embryo depictions:
Figure 15-15 Comparison of the embryonic
development of a fish, an amphibian, a bird, and a
mammal. The early stages (_above_) are closely
similar; the later stages (_below_) are more divergent.
The earliest stages are drawn roughly to scale; the later
stages are not (After E. Haeckel, The Evolution of Man.
London, 1879.)
Question: When was it first widely known that Haeckel's
embryo depictions were fraudulent?
Compare the above 1983 Alberts with:
[1956 Goldschmidt]"Real trouble was in store for him
[Haeckel] when he once more returned to a popular
presentation of his monistic evolutionary philosophy in his
book _The Riddle of the Universe_. Compared with this, his
previous books were only mild statements. In an aggressive,
fanatic spirit he presented his solutions for all riddles of
matter and mind, bridging difficulties with bland assertions.
Even his friends were shocked by the superficiality of his
arguments and the sloppy handling of the facts. A real storm
brewed when he was accused of having falsified pictures of
embryos which were to prove the absence of differences in
animal and human development. There was no doubt that the
originals had been tampered with in the reproduction, though
an exact copy would have been just as good for illustrating
his argument. It may be considered as certain that Haeckel
did not intend any falsification for which there was no
reason. He had simply indulged in his old tendency to
conventionalize his drawings and to make them approach an
ideal picture he had in his mind. This is, of course, not an
excuse for a naturalist, who should reproduce nature
faithfully. There was a great outcry from philosophers and
theologians, joined also by some of his colleagues,
demanding Haeckel's removal from his chair with the
Socratic indictment of corruptor of youth. But the protector
of Jena University, the Grand Duke of Saxe-Weimar, proud
of the enlightened tradition of his family and personally
friendly to Haeckel, refused to interfere with the professor's
right to his opinions and his responsibility for his writings.
After all, Haeckel and his house in Jena had become a kind
of European institution."
Politics triumphed over truth, which then slumbered.
Question: Where else in the history of the "theory of evolution" has
politics suppressed truth?
Section "EMBRYOLOGY & FRAUD" in
Fatally Flawed: Vestigial Organs, Biogeography, Homology,
and Embryology as Evidence for the Theory of Evolution
http://groups.google.co.in/groups?selm=Pine.SGI.4.44L.01.0305250118100.2340516-100000%40irix2.gl.umbc.edu
Wells, Jonathan. 2000. _Icons of Evolution: Science or
Myth?: Why Much of What We Teach about Evolution Is
Wrong_ (USA: Regnery Publishing, Inc.), 338pp., chapter 5
"Haeckel's Embryos."
Goldschmidt, Richard B. 1956. _Portraits from Memory:
Recollections of a Zoologist_ (Seattle: University of
Washington Press), 181pp. On 31-40, the section on
Haeckel:
I had the good luck to see a little more of Ernst Haeckel,
one of the most amazing and most controversial figures
German science has produced. The present generation
cannot imagine the role he played in his time, far
beyond his actual scientific performance. Haeckel was
one of the students of Johannes Muller and thus the first
to help in founding the dynasty of zoologists, already
mentioned, near the end of which I find myself. Like
most zoologists of those days he studied medicine, and
he took his M.D. with a thesis containing a great
discovery: the amoeboid movement of the lymphocytes
(in the blood of the crayfish). He hung out his shingle,
and, when it turned out that no patients appeared at the
visiting hours from 7:00 to 8:00 A.M., he gave up and
became what he wanted to be, a zoologist. Johannes
Muller had initiated his students into marine zoology.
He loved to go to the Mediterranean, settle in some
fishing village, hire a boat and an empty shack as a
laboratory, and start a study of the rich treasures which
were to be found all around. Haeckel chose the study of
the medusae and later of the radiolaria. His big
monographs on these groups are still basic for their
taxonomy and morphology. They are actually almost
the only factual contributions Haeckel made to zoology,
enough to secure him a professorship in Jena but not
enough for his later fame, which was based upon a
completely different performance.
In this, his morphological and taxonomic work, Haeckel
already showed a gift and a tendency which were to get
him into trouble later. He had a great facility in
draftsmanship and for some time had thought of
becoming a painter. As a matter of fact, he would have
been a very poor Victorian painter, as can be seen from
samples of his work, some of which he published with
his travel books on Ceylon and Java. Others I saw in his
house. They were mere illustrations, well executed but
completely conventional and uninteresting and without
any artistic merit. Actually Haeckel, in his later life, had
a chance to demonstrate his lack of genuine artistic
feeling when he violently opposed the frescoes which
the great Swiss Ernst Hodler painted for the University
in Jena, his admirable "Departure of the Students" in the
Napoleonic wars. But to return to the illustrations of his
monographs, Haeckel's easy hand at drawing made him
improve upon nature and put more into the illustrations
than he saw. His medusae assumed romantic
movements. One new species he called _Mitrocoma
annasethe_ (the nightbonnet of Anna Sethe, his wife)
because the tentacles flowing from the umbrella
reminded him of his wife's hair bursting out of her
bonnet. The drawing shows the tentacles in such a way
as to fit this comparison. Similarly Haeckel's radiolaria
were too perfect all over. One had the impression that
he first made a sketch from nature and then drew an
ideal picture as he saw it in his mind.
Haeckel's genius, with all its different facets, came out
first when he wrote his theoretical magnum opus under
the influence of the _Origin of Species_, which started
him on his career as Darwin's greatest apostle on the
continent. The two volumes of the _Generelle
Morphologie_ established the basis of evolutionary
thinking in morphology. The work pried into the
workings of evolution in establishing the forms of
animals. It put into the center the law of recapitulation,
which Haeckel called the _biogenetisches Grundgesetz_,
and tried to work out a phylogeny of form based upon
this law. The importance of the work for the subsequent
development of evolutionary morphology becomes
evident if we mention only a few of the terms he
introduced: ontogeny, phylogeny, gastrula, blastula,
morula, protista. It established many of the ideas on
growth, form, symmetry, and such basic elements of
morphology, and many of these ideas as well as the new
terms have been incorporated into elementary zoology.
But with this great effort and the already mentioned
monographs, to which later the big volume on the
radiolaria of the "Challenger" Expedition were added,
Haeckel's original contributions to zoology end, except
for a long work on systematic phylogeny, the value of
which is doubtful. From then on he was only the
unflinching, fanatic apostle of evolution as he saw it and
of the philosophy of monism, which he considered to be
the logical consequence of Darwinism. This role he
assumed and established in his two major popular
books, the _Natural History of Creation_ and
_Anthropogeny_.
The present generation can hardly understand the
influence Haeckel exercised through these books upon
the minds of youth, of laymen in general, and also upon
large sections of the professional world. Perhaps I may
describe it best by my own experience. When I was a
high school boy of about sixteen, I found myself in a
period of doubt and revolution against traditional
religion, a condition which was rather typical for the
educated youth at that time. While in this stage, I got
hold of some literature (paralleled somewhat in this
country by Ingersoll's writings) which violently attacked
traditions and commended an extreme materialistic
philosophy. My father was a member of a citizens' club
which owned a very large library, run as a lending
library for the members. Once a week or so, I was sent
there to exchange my parents' books, which meant that I
went to the stacks to pick out what my parents wanted.
The books were then presented to the librarian for
registration. Of course, once in the stacks, I began to
browse and to look for books which might satisfy my
interests, and thus I struck the revolutionary books by
Karl Vogt and the wild _Energy and Matter_ of
Buchner, a kind of atheistic Bible. As I could not dare
to bring home such books openly, I hid them under my
coat, read them secretly, and returned them to the
shelves the same way, some weeks later. In this way I
found Haeckel's history of creation one day and read it
with burning eyes and soul. It seemed that all problems
of heaven and earth were solved simply and
convincingly; there was an answer to every question
which troubled the young mind. Evolution was the key
to everything and could replace all the beliefs and creeds
which one was discarding. There were no creation, no
God, no heaven and hell, only evolution and the
wonderful law of recapitulation which demonstrated the
fact of evolution to the most stubborn believer in
creation. I was so fascinated and shaken up that I had to
communicate to others my new knowledge, and this was
done in the school yard, on school picnics, and among
friends. I remember vividly a scene during a school
picnic when I stood surrounded by a group of
schoolboys to whom I expounded the gospel of
Darwinism as Haeckel saw it. Another boy, who was
already destined to become a parson like his father,
passed and remarked, "He is again at converting."
Indeed my zeal, which was Haeckel's zeal, was that of a
missionary. I might be excused because of my age, but
Haeckel never ceased to be a fanatic, bigoted zealot for
his philosophy of monism. It was at that time that I
gave my first talk on evolution (of course a dramatic
digest of Haeckel) before a boys' club. I wish I had a
copy of this performance.
There is no doubt that hundreds of thousands, young and
old, inside and outside Germany, were impressed in the
same way, and that thus Haeckel became one of the
most beloved and most hated men of his time. For many
years he must have spent most of his working hours
writing polemic pamphlets against his critics, and some
of these are quite amazing. He produced only one more
scientific book, as has already been mentioned, a
systematic phylogeny in which he tried to develop his
somewhat naive type of evolutionary trees for the whole
living world, freely inventing ancestral groups where he
needed them.
Real trouble was in store for him when he once more
returned to a popular presentation of his monistic
evolutionary philosophy in his book _The Riddle of the
Universe_. Compared with this, his previous books
were only mild statements. In an aggressive, fanatic
spirit he presented his solutions for all riddles of matter
and mind, bridging difficulties with bland assertions.
Even his friends were shocked by the superficiality of
his arguments and the sloppy handling of the facts. A
real storm brewed when he was accused of having
falsified pictures of embryos which were to prove the
absence of differences in animal and human
development. There was no doubt that the originals had
been tampered with in the reproduction, though an exact
copy would have been just as good for illustrating his
argument. It may be considered as certain that Haeckel
did not intend any falsification for which there was no
reason. He had simply indulged in his old tendency to
conventionalize his drawings and to make them
approach an ideal picture he had in his mind. This is, of
course, not an excuse for a naturalist, who should
reproduce nature faithfully. There was a great outcry
from philosophers and theologians, joined also by some
of his colleagues, demanding Haeckel's removal from
his chair with the Socratic indictment of corruptor of
youth. But the protector of Jena University, the Grand
Duke of Saxe-Weimar, proud of the enlightened
tradition of his family and personally friendly to
Haeckel, refused to interfere with the professor's right to
his opinions and his responsibility for his writings.
After all, Haeckel and his house in Jena had become a
kind of European institution.
When I first met Haeckel he was already a
septuagenarian. When Richard Hertwig brought him to
my room I knew at once, from the many pictures I had
seen, who the visitor was. His was a most conspicuous
and impressive appearance. He must have been six and
a half feet tall, with an erect, athletic body. On his
shoulders sat an unusually large head, with a broad,
high-arched forehead, surrounded by a white mane
which continued into a long white beard. He wore the
usual professor's wide-brimmed fedora which for him
had to be made to order, since no store kept such a large
hat size. Seeing him with his hat on, one thought at
once of the Teutonic god Wotan. But while that
embattled god had one eye covered, Haeckel looked at
you with sparkling, boyish eyes of the most brilliant
sky-blue I ever saw. But then came the disappointment;
when he started speaking he spoke in a high pitch,
completely out of tune with the huge body. His
temperament was immense, and he was constantly on
the move. But what he said was rather disappointing. I
was working at that time, almost fifty years ago, with
the strange, partly neotenic larval forms of tropical
_Amphioxus_ species described as _Amphioxides_ and
had indulged in some (not so good) phylogenetic
speculations. I showed Haeckel some slides, but his
comments showed that his ideas were still those of the
naive phylogeny of his youth.
The last time I saw Haeckel he was past eighty and in
bad shape. He had broken his hip, and though it had
healed he was condemned to an armchair in his house.
He complained bitterly, as his still fiery temperament
made it hard for him to keep quiet. In addition he had
gone through some bitter disappointment. In his older
days he had spent much time upon building and
establishing a phyletic museum which a rich admirer,
Ritter, had endowed. Here he wanted to exhibit
evolution, as he saw it, as a kind of Darwinian shrine for
freethinkers. When the time of his retirement came, his
great wish was to have a successor who would build up
this museum according to his ideas. His eyes fell upon
Ludwig Plate, who had written a rather good book on
Darwinism, was an all-around zoologist with experience
in collecting abroad, and had begun to dabble with the
genetics of mice. In spite of warnings against this
notorious bully, Pan-Germanist, and racist, Haeckel
insisted on making him his successor. It did not take
long until Plate pushed Haeckel out of his museum,
where he had still kept a room, and actually forbade him
to enter the building. To make matters worse, Plate
formally accused Haeckel of having stolen books
belonging to the university. Haeckel had given his
private library to the museum, and it seems that when he
was driven out he took some of what had been his own
books to his house. On this Plate based his public
accusation. I, myself, have read Haeckel's letters to
Richard Hertwig, reporting on his misery. Hertwig,
Haeckel's former student, wrote to his own former
student, Plate, and asked him to behave better toward
the grand old man, drawing his attention to the
unanimous condemnation of his actions by all decent
people. This letter I read also. But Plate refused to
budge, and thus Haeckel's last years were very unhappy.
While I am mentioning the doings of this unpleasant
character Plate, I cannot help inserting the story of a
scene which I witnessed and which characterizes well
the brutal type he represented. At a meeting of the
zoological society Professor Plate had announced a
paper on a remarkable elephant embryo. Before the
meeting I was looking at some exhibits with Spemann
when we were joined by Plate who offered to show us
his elephant embryo. He produced a jar of about five by
ten inches which contained a completely developed
fetus the size of a newborn puppy, covered with dark
hair, showing long claws on all toes, and having a
proboscis-like protrusion one or two inches long at the
head. Plate told us that he had been so lucky as to buy
the precious specimen from an Arab near the Red Sea
and then raved about the immense phylogenetic
importance of the specimen, especially the hair and
claws. Spemann took a good look and asked Plate what
it meant that the embryo had only a single large median
eye which in addition was located below the proboscis
where the mouth should be. Spemann saw at once that
the specimen was a cyclopean monster, a kind of freak
which frequently has a single eye below the nose, which
might grow out proboscis-like. The elephant embryo of
the clever Arab was a cyclopean dog (or jackal) embryo.
Did this silence Plate? Not at all. The next day he
presented without wincing a paper on a cyclopean
monster of a dog which might be mistaken for an
elephant fetus!
=========================================.
Highlights and for Further Reading
"He produced only one more scientific book, as has already
been mentioned, a systematic phylogeny in which he tried to
develop his somewhat naive type of evolutionary trees for
the whole living world, freely inventing ancestral groups
where he needed them."
"to return to the illustrations of his monographs, Haeckel's
easy hand at drawing made him improve upon nature and put
more into the illustrations than he saw. His medusae
assumed romantic movements. .... One had the impression
that he first made a sketch from nature and then drew an
ideal picture as he saw it in his mind."
"started him on his career as Darwin's greatest apostle on the
continent. The two volumes of the _Generelle Morphologie_
established the basis of evolutionary thinking in morphology.
The work pried into the workings of evolution in establishing
the forms of animals."
T0E good for study of morphogenesis?: Goodwin
http://groups.google.co.in/groups?selm=b1c67abe.0402230503.56fa7a7%40posting.google.com
"The present generation can hardly understand the influence Haeckel
exercised through these books upon the minds of youth, of laymen
in general, and also upon large sections of the professional
world. .... When I was a high school boy of about sixteen, I found
myself in a period of doubt and revolution against traditional
religion, a condition which was rather typical for the
educated youth at that time."
"once in the stacks, I began to browse and to look for books
which might satisfy my interests, and thus I struck the
revolutionary books by Karl Vogt and the wild _Energy and
Matter_ of Buchner, a kind of atheistic Bible."
Einstein: physics was designed
http://groups.google.co.in/groups?selm=dford3-37f67dF59po8jU1%40individual.net
"In this way I found Haeckel's history of creation one day
and read it with burning eyes and soul. It seemed that all
problems of heaven and earth were solved simply and
convincingly; there was an answer to every question which
troubled the young mind. Evolution was the key to
everything and could replace all the beliefs and creeds which
one was discarding. There were no creation, no God, no
heaven and hell, only evolution and the wonderful law of
recapitulation which demonstrated the fact of evolution to the
most stubborn believer in creation. I was so fascinated and
shaken up that I had to communicate to others my new
knowledge, and this was done in the school yard, on school
picnics, and among friends. I remember vividly a scene
during a school picnic when I stood surrounded by a group of
schoolboys to whom I expounded the gospel of Darwinism
as Haeckel saw it. Another boy, who was already destined to
become a parson like his father, passed and remarked, "He is
again at converting." Indeed my zeal, which was Haeckel's
zeal, was that of a missionary. I might be excused because of
my age, but Haeckel never ceased to be a fanatic, bigoted
zealot for his philosophy of monism. It was at that time that
I gave my first talk on evolution (of course a dramatic digest
of Haeckel) before a boys' club. I wish I had a copy of this
performance."
1937 Goldschmidt on winning souls for Darwin
http://groups.google.co.in/groups?selm=b1c67abe.0403131825.1eefa6ee%40posting.google.com
"From then on he was only the unflinching, fanatic apostle of
evolution as he saw it and of the philosophy of monism,
which he considered to be the logical consequence of
Darwinism."
Darwin only talks to and through his prophets.
http://groups.google.co.in/groups?selm=dford3-37f8trF5cdutnU1%40individual.net
"he had spent much time upon building and establishing a
phyletic museum which a rich admirer, Ritter, had endowed.
Here he wanted to exhibit evolution, as he saw it, as a kind of
Darwinian shrine for freethinkers."
"In spite of warnings against this notorious bully,
Pan-Germanist, and racist, Haeckel insisted on making him
[Ludwig Plate] his successor."
phrase "spontaneous generation" used by Haeckel, Wald,
Barrow & Tipler, and Dawkins
http://groups.google.co.in/groups?selm=dford3-b1c67abe.0408230552.47df9705%40posting.google.com
how do blindwatchmakingists "know" that life came from
non-life via non-intelligence-directed processes?:
Haeckel; Goodrich; Wells, J. Huxley, & Wells;
Simpson; Sagan; Dawkins; Johnson (a creationist)
http://groups.google.co.in/groups?selm=Pine.SGI.3.96A.990812214926.974808E-100000%40umbc8.umbc.edu
Dobzhansky, 1900 Haeckel ("the law of the persistence of
matter and force; that law knows nothing of a beginning"),
and 1987 Dawkins reject the position that intelligent design
is responsible for common descent
http://groups.google.co.in/groups?selm=b1c67abe.0401311740.48df353%40posting.google.com
Haeckel on murdering the disabled
http://groups.google.co.in/groups?selm=b1c67abe.0407271740.7ae3b80b%40posting.google.com
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| User: "Tracy Hamilton" |
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| Title: Re: The Misrepresentations of Richard Forrest |
02 Mar 2005 03:34:17 PM |
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"david ford" <dford3@gl.umbc.edu> wrote in message
news:dford3-38m3vrF5o7bk2U1@individual.net...
Tracy Hamilton <DontSpamhamilton@uab.edu> on 28 Feb 2005:
david ford <dford3@gl.umbc.edu> wrote in message
news:dford3-38hcs9F5ovk6pU1@individual.net...
Larry Moran wrote:
On 22 Feb 2005 Seanpit
<seanpitnospam@naturalselection.0catch.com> wrote:
Paul J Gans,
I don't have much time today to respond to nonsense, but this was
just
too hilarious to pass up. You wrote:
[*] Could you please stop with this "amino acid" crap? There
are NO amino acids present in a protein. There are entities
that could be amino acids if they existed freely.
Oh really?! What do you call the individual molecules that "used
to be
amino acids" when they are linked together in a peptide chain?
Hint:
amino acids.
I call them *amino acid residues* or just
plain *residues* and so do most
other biochemists.
What approximate percentage of
1) biologists, and
2) biochemists,
use "amino acids" in their verbal and e-mail conversations?
4 out of 5 biochemists. The fifth is temporarily dazed from
trying to make sense of the muddle that is Sean Pitman's
proposals.
I hope Larry doesn't stay [TH]"dazed" for long, since I
eagerly await new posts of his.
What approximate percentage of biologists use "amino acids" in their
verbal and e-mail conversations?
More than biochemists would, since biologists are not famous
for their technical understanding of biochemistry. And vice versa.
When Mathews & van Holde wrote of an
[M&vH]"amino acid sequence," did they use [TH]"proper
terminology"?:
Mathews, Christopher K. and K. E. van Holde. 1990.
_Biochemistry_ (USA: The Benjamin/Cummings Publishing
Co., Inc.), 1129pp. On 148:
Every protein has a defined order of amino acid
residues. As with the nucleic acids, this sequence is
referred to as the _primary structure_ of the protein.
Figure 5.14 shows the amino acid sequence of sperm
whale myoglobin, the protein whose structure we saw in
Figure 5.1.
There is a difference between "amino acids" and "amino acid
sequence".
Perhaps you can figure out what it is, perhaps you can't. I
will throw in three clues - amide, acid, amine.
Go to an organic chemistry text, and see if it treats amides in the same way
as amines and carboxylic acids.
Note another term in just this little paragraph that Sean Pitman
does not use, when he should: primary structure. It has
a specific meaning. I also do not recall Pitman discussing secondary,
tertiary, or quaternary structure. These are CRUCIAL determinants of
protein function, and any discuss of function that does not include this
is only babble!
While going down this little rabbit hole, I decided to look at the amino
acid and
protein chapter in Morrison and Boyd, 3rd Ed. There were only four
elements
when this book was written - air, earth, water and fire. Anyhow, it should
be noted that
they are careful in their terminology, using amino acid residue, amino acid,
and
primary structure in the same way as biochemists today.
[snip]
[LM]"biochemistry textbooks... are much more reliable sources of
information than web pages"
Shapiro, Robert. _Origins: A Skeptic's Guide to the Creation
of Life on Earth_ (GB: Penguin Books, 1986), 332pp.
On 108:
[snip - nothing about using residues vs amino acids for proper
terminology,
nor from a biochemistry text, nor from even a recent biochemistry
text]
Before you snipped Shapiro, did you read it?
Yes. That is how I knew it was irrelevant to "amino acid" vs
technically correct terminology for peptide residues.
Shapiro had
quoted [TH]"from a biochemistry text" and pointed out the
erroneousness of the claim that that biochemistry text made.
Compare [LM]"biochemistry textbooks... are much more reliable sources of
information than web pages"
BTW, Larry quoted from that same textbook in the post to which
I replied.
Much more reliable is not the same thing as infallible or complete.
If you can't tell the difference between the reliability of a text
on basic terminology and concepts that are used by the
researchers in the field (who learned their terminology from textbooks),
and a web page that google decided to give you in a search, then you
are incapable of exercising judgement. I recommend you do not
avial yourself of any business opportunities from ex-Nigerian
government officials.
I've told my students that if they rely on the world wide web for
their
information they might be given a failing grade.
Even if it's from the website http://www.talkorigins.org ?
Where on the web can I read "Laurence Moran's Evolution Home Page"?
If that is all a student writing a report on evolution cites for
explaining
it,
he had damn well get an F! Why do you think there are references on
talk.origins? For people to ignore?
Please rephrase your question without using the word "why."
It was perfectly clear as written.
Note that these are to biology
textbooks, just like
he was referring anybody wanting to know the proper terminology in
biochemistry he used biochemistry textbooks.
You are not very good at this - give it up!
[LM]"Google gets you crap." I did a Google search for:
Laurence Moran evolution
Are these Google-found webpages [LM]"crap"?:
http://www.talkorigins.org/faqs/evolution-definition.html
No. But I can tell you a guaranteed way to get crap. Do a google
groups search for author Ford, David. Actually, we don't need to do
this,
do we? You do it often enough for us.
And you, Tracy, do a marvelous job of shooting it down.
What is your response to this post?:
Ahem, I believe that we left a discussion that tried to get
you to reveal your understanding about natural selection.
What is your response to this post?
http://groups-beta.google.com/group/talk.origins/msg/70ccb18bb5d99c90
There was one "response" that was not a response, but a claim that
it was answered in another link. Sorry, we're not buying evasion right
now - we seem to have a surplus. What we need is clarity. A request to
remove ambiguity was ignored by you. That speaks way more about you
than you realize.
Would you give any of these Larry Moran remarks [LM]"a failing grade,"
and if so, which ones?:
LM in
http://groups.google.co.in/groups?selm=7br95q%24efv%241%40bioinfo.med.utoronto.ca
Maybe you could write a paragraph or two describing
to students how the protein folding problem was solved
and how you envisage the formation of a well defined
three dimensional structure from a linear chain of amino
acids.
It sounds like a good question to me. What do you know about the
protein folding problem? Apparently - NOTHING!
Nothing new there.
[further snippage - it is more of the same level, or worse]
In the Larry quotations you snipped, do you think Larry
used [TH]"proper terminology" with regards to
[TH]"using residues vs amino acids"?
Ah, I see your idiotic point.
None of Larry's comments were in the least ambiguous nor
vague, if you know biochemistry.
You mentioned biology textbooks. Do you consider this
Alberts and its accompanying figure [LM]"reliable"?:
Alberts, Bruce, Dennis Bray, Julian Lewis, Martin Raff,
Keith Roberts, James D. Watson. 1983. _Molecular Biology
of the Cell_ (USA: Garland Publishing, Inc.), 1146 + 35pp.
On 825, a caption that accompanies a rendering of Haeckel's
fraudulent embryo depictions:
Figure 15-15 Comparison of the embryonic
development of a fish, an amphibian, a bird, and a
mammal. The early stages (_above_) are closely
similar; the later stages (_below_) are more divergent.
The earliest stages are drawn roughly to scale; the later
stages are not (After E. Haeckel, The Evolution of Man.
London, 1879.)
Question: When was it first widely known that Haeckel's
embryo depictions were fraudulent?
I know this is a red herring, but do you know what is fraudulent
about Haeckel's drawings? Just curious. No quotes, in your
own words such as "all drawn upside down" or something easy
to follow.
[massive snip]
Tracy P. Hamilton
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| User: "Richard Forrest" |
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| Title: Re: The Misrepresentations of Richard Forrest |
28 Feb 2005 03:39:02 PM |
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david ford wrote:
<snipped>
Sorry David, but
Dz~abbersmok
Maciej S/lomczyński
Byl/o smaszno, a jaszmije smukwijne
S´widrokre¸tnie na zegwniku we¸z~al/y,
Peliczaple stal/y smutcholijne
I zbl/a¸kinie rykos´wista¸kal/y.
"Ach, Dz~abbersmoka strzez~ sie¸, strzez~!
Szponów jak kl/y i tna¸cych szcze¸k!
Drz~yj, gdy nadpel/ga Banderzwiez~
Lub Dz~ubdz~ub ptakoje¸k"
W dl/oń uja¸l/ migbl/ystalny miecz,
Za swym pogromnym wrogiem mknie...
Stl/umiwszy gniew, ws´ród Tumtum drzew
W zadumie ukryl/ sie¸.
Gdy w czarsmuts´leniu cichym stal/,
Pl/omiennooki Dz~abbersmok
Zagrzmudnil/ pos´ród sroz~nych skal/,
Sapgulcza¸c poprzez mrok!
Raz-dwa! Raz-dwa! I ciach! I ciach!
Miecz migbl/ystalny s´wistotnie!
Leb ucia¸l/ mu, wzia¸l/ i co tchu
Galumfuja¸co mknie.
"Cudobry mój, us´cisńij mnie,
Gdy Dz~abbersmoka s´cia¸l/ twój cios!
O wielny dniu! Kalej! Kalu!"
s´mieselil/ sie¸ rad w gl/os.
Byl/o smaszno, a jaszmije smukwijne
S´widrokre¸tnie na zegwniku we¸z~al/y,
Peliczaple stal/y smutcholijne
I zbl/a¸kinie rykos´wista¸kal/y.
RF
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| User: "maff" |
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| Title: Re: The Misrepresentations of Richard Forrest |
28 Feb 2005 04:11:42 PM |
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david ford wrote:
[...]
Nah. It's still scientifically illiterate Christian fascist apologetics.
.
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| User: "Glenn" |
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| Title: Re: The Misrepresentations of Richard Forrest |
28 Feb 2005 05:38:57 PM |
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"maff" <maff91@yahoo.com> wrote in message
news:1109628702.716112.290740@o13g2000cwo.googlegroups.com...
david ford wrote:
[...]
Nah. It's still scientifically illiterate Christian fascist apologetics.
"Maff", you're sick. Seek help.
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| User: "maff" |
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| Title: Re: The Misrepresentations of Richard Forrest |
01 Mar 2005 05:06:50 AM |
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Glenn wrote:
"maff" <maff91@yahoo.com> wrote in message
news:1109628702.716112.290740@o13g2000cwo.googlegroups.com...
david ford wrote:
[...]
Nah. It's still scientifically illiterate Christian fascist
apologetics.
"Maff", you're sick. Seek help.
Are you projecting?
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| User: "josephus" |
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| Title: Re: The Misrepresentations of Richard Forrest |
01 Mar 2005 07:51:26 AM |
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maff wrote:
Glenn wrote:
"maff" <maff91@yahoo.com> wrote in message
news:1109628702.716112.290740@o13g2000cwo.googlegroups.com...
david ford wrote:
[...]
Nah. It's still scientifically illiterate Christian fascist
apologetics.
"Maff", you're sick. Seek help.
Are you projecting?
David Ford is really trying to upgrade his ignorant ranting. He really
doesn't have a clue. He never really says zanying new or even
interesting.
Definition: Religiosity: Mental aberration characterized by extreme
rigid thing and delusions about religion. Remember the Jesus Freaks.
Their belief system approximated religiosity. The current day
fundamentalists are a pale echo.
josephus
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| User: "david ford" |
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| Title: Re: The Misrepresentations of Richard Forrest |
02 Mar 2005 09:26:54 AM |
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Glenn wrote:
"maff" <maff91@yahoo.com> wrote in message
news:1109628702.716112.290740@o13g2000cwo.googlegroups.com...
david ford wrote:
[...]
Nah. It's still scientifically illiterate Christian fascist apologetics.
"Maff", you're sick. Seek help.
Glenn, it's okay. Maff is still sore about the fact that Einstein
didn't remain an atheist.
Einstein: physics was designed
http://groups.google.co.in/groups?selm=dford3-37f67dF59po8jU1%40individual.net
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| User: "Steve Mading" |
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| Title: Re: The Misrepresentations of Richard Forrest |
02 Mar 2005 12:50:06 PM |
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On Wed, 02 Mar 2005 10:26:54 -0500,
david ford <dford3@gl.umbc.edu> wrote:
Glenn wrote:
"maff" <maff91@yahoo.com> wrote in message
news:1109628702.716112.290740@o13g2000cwo.googlegroups.com...
david ford wrote:
[...]
Nah. It's still scientifically illiterate Christian fascist apologetics.
"Maff", you're sick. Seek help.
Glenn, it's okay. Maff is still sore about the fact that Einstein
didn't remain an atheist.
People who lie as much as you do don't deserve any modicum of respect.
This point has been gone over with you time and time again, and
countered time and time again, and you still act like we've never
been able to reply to you and shoot it down.
.
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| User: "david ford" |
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| Title: Re: The Misrepresentations of Richard Forrest |
02 Mar 2005 09:14:40 PM |
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(Steve Mading) wrote in message news:<slrnd2c246.i75.>...
On Wed, 02 Mar 2005 david ford <dford3@gl.umbc.edu> wrote:
Glenn wrote:
"maff" <maff91@yahoo.com> wrote in message news:1109628702.716112.290740@o13g2000cwo.googlegroups.com...
david ford wrote:
[...]
Nah. It's still scientifically illiterate Christian fascist apologetics.
"Maff", you're sick. Seek help.
Glenn, it's okay. Maff is still sore about the fact that Einstein
didn't remain an atheist.
People who lie as much as you do don't deserve any modicum of respect.
What are 3 of these supposed many-lies of mine?
Do you think Haeckel [SM]"deserve[s] any modicum of respect"?
1983 Bruce Alberts; Haeckel's fraudulent embryo depictions; 1956 Goldschmidt
http://groups.google.co.in/groups?selm=dford3-38m3vrF5o7bk2U1%40individual.net
This point has been gone over with you time and time again, and
countered time and time again, and you still act like we've never
been able to reply to you and shoot it down.
Remind me, what [SM]"point" are you referring to?
Einstein to zu Lowenstein, year unknown, cited in
Jammer, Max. 1999. _Einstein and Religion: Physics and
Theology_ (USA: Princeton University Press), 279pp., 96-97:
In view of such harmony in the cosmos which I, with
my limited human mind, am able to recognize, there are
yet people who say there is no God. But what really
makes me angry is that they quote me for support of
such views.
More Einstein is in
Einstein: physics was designed
http://groups.google.co.in/groups?selm=dford3-37f67dF59po8jU1%40individual.net
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