Salisbury's Doubts about the Synthesis
david ford
Synthetic Theory of Evolution" _The American Biology Teacher_,
335-338, 354.
The author prepared this essay for his textbook of botany (of which
William A. Jensen, of the University of California at Berkeley, is
senior author), to be published by Wadsworth Publishing Co., Belmont,
Calif. Salisbury is professor of plant physiology, Plant Science
Dept., College of Agriculture, Utah State University, Logan 84321.
Could our modern synthetic theory of evolution be wrong, as were its
predecessors, evolution through the inheritance of acquired characters
(Lamarck) and instant new species by mutations (De Vries)? What will
scientists say a hundred years from now about Neodarwinism, the
current theory?
I have my doubts about one point in the concept. Of course, that
isn't bad; it is how science progresses. Someone doubts an accepted
point, and other scientists, being fundamentally conservative about
the things they have learned, immediately pounce on the doubter
(providing the point he brings up can be taken seriously). Eventually
this leads to one of two situations, both of them good for science:
either the doubter is proven wrong or he is proven right. If he is
wrong, much will have been learned in marshaling the facts required to
settle the question. If he is right, whole new areas of understanding
may have been opened. My particular doubt has been published
(Salisbury, 1969), scientists have taken their shots at it (Smith,
1969), and it has been defended (Spetner, 1970).
The Origin of Variability
The problem is the origin of variability. Both Lamarck and De Vries
put forth their theories to account for this. Darwin was fully aware
of the seriousness of the problem, and he retreated with misgivings to
Lamarck's ideas. The modern theory emphasizes the importance of
genetic recombinations but ultimately rests upon mutations as the
source of the variability acted upon by natural selection. This is
where I run into problems.
First, let me emphasize that it is quite foolish to doubt most of the
evolutionary story. The fossils are there, and their mute testimony
is overwhelming evidence that numerous forms of life have existed on
earth over immense spans of time. Furthermore, the most primitive
ones existed at [the] earliest times, the most complex ones most
recently. Fundamentalist writers and others have tried to provide
reasonable alternative explanations for the fossils, but these are
never convincing. Furthermore, the mechanism of natural selection as
described by Darwin and the modern embellishments upon it provided by
population geneticists can hardly be questioned. Gene frequencies do
change in populations as a result of selection pressures. This has
been observed in the field and duplicated in the laboratory. No
scientific fact could be demonstrated more clearly.
But will changes in gene frequencies in response to selection
pressures account for evolution in the broadest sense: life
originating in the ancient soupy seas and developing over eons of time
until the earth is covered with flowering plants and thinking men?
_Only if there is a continual source of new genes for selection to act
upon._ If, somewhere back in the dim reaches of time, a cell evolved
the process of photo-synthesis, it is because, according to the
present theory, the proper genes and their enzymes were there for
selection to act upon. Could random changes in the nucleotide
sequences of DNA (mutations) provide these genes and ultimately the
enzymes? At the moment, I doubt it, and my reasons for doubting are
based upon discoveries during the past 20 years that have indicated to
us how really complex living systems are. We have known for a long
time that man's body is an intricate and complex machine. Now we know
that the cell itself is far more complex than we had imagined. It
includes thousands of functioning enzymes, each one of them a complex
machine itself. Furthermore, each enzyme comes into being in response
to a gene, a strand of DNA. The information content of the gene (its
complexity) must be as great as that of the enzyme that it controls.
One might begin (as I did) to get the intuitive feeling that genes and
enzymes are too complex to originate by randomly changing nucleotide
sequences. But intuitive feelings are often wrong and never really
satisfying. How can we pin it down?
How Many Genes Could Exist?
It is possible to get a numerical idea of the complexity of genes and
enzymes by considering the possible number that could exist. This is
easy. Proteins (enzymes) consist of 20 different kinds of amino
acids. If the "protein" consisted of only one amino acid, then there
could be 20 kinds; if two amino acids, then each of the first 20 could
combine with any of another 20, so there could be 20 x 20 = 400 kinds.
Each time we add an amino acid link to the chain we have 20
possibilities to choose from, and so we multiply by 20. If there are
10 amino acids in the chain, then there can be 20^10 (20 multiplied by
itself 10 times = 204.8 trillion) kinds of amino acid chains.
The same thing applies to language, which, in a general sense, is any
form of information consisting of individual information bits. In the
English language, we can imagine that there might be 30 different
characters (26 capital letters, a space, quotation marks, a colon, and
a period, for example). Choosing from these characters, we can write
the following sentence from Shakespeare: "THIS ABOVE ALL: TO THINE
OWN SELF BE TRUE." Could we write this sentence by allowing monkeys
to pound typewriters randomly or by blowing up a printshop and then
searching for the sentence among the bits of type on the street?
Let's build small computers instead. Each one occupies a volume of 1
l, and all are connected. They cover all the earth to a depth of 2
km. Each one changes a character in a sequence of 45 characters and
compares the result with the sentence above. It does this a trillion
times each second, and no two computers ever duplicate their efforts.
To try more sentences, we cover 10^20 identical planets to a depth of
2 km with such computers, still programming them so that no two ever
duplicate the same sequence of characters. Now we let the computers
on all these planets run for four billion years, the time required to
form all possible 45 character-sequences ("sentences"), using 30
characters: 1.3 x 10^67 sequences. One of these will be our
Shakespearean sentence-- causing the proper red light to come on! Of
course, the light could have come on during the first second of the
billion-year period or during the last, but to try all possible
combinations requires all the computers on all the planets and all the
time. Such an example helps one realize that 10^67 is a truly large
number.
Yet it is small compared to the possible numbers of genes and enzymes.
A medium protein might include about 300 amino acids. The DNA gene
controlling this would have about 1,000 nucleotides in its chain.
Since there are four kinds of nucleotides in a DNA chain, one
consisting of 1,000 links could exist in 4^1000 different forms.
Using a little algebra (logarithms), we can see that 4^1,000 = 10^600.
Ten multiplied by itself 600 times gives the figure 1 followed by 600
zeroes! This number is completely beyond our comprehension. Assume,
for example, a cubic universe with dimensions of 20 billion (2 x
10^10) light-years on each side. In angstroms, the smallest unit used
by scientists, this becomes about 10^39 A on a side, with a volume of
"only" 10^117 A^3. Since our DNA chain requires over half a million
A^3 of space, imagine how many universes it would take to accommodate
10^600 DNA chains!
A Mechanism of Chemical Evolution
Norman Horowitz (1945) proposed a mechanism of chemical evolution of
metabolic systems. Imagine that the primeval ocean contained
virtually all of the common precursors for life processes: sugars,
amino acids, fats, nucleotides, etc. Imagine that a cell containing a
reproducing DNA chain had come into being and that this could control
the synthesis of specific enzymes; that is, that life had come into
being. But imagine this to be a highly heterotrophic form of life,
able to synthesize none of the precursors required for its existence
but obtaining them all from the primeval ocean. Our original cell
will multiply until this ocean is overpopulated and the food supply
limited. The fittest cell will then survive; namely, one that
contains an enzyme capable of converting a molecule present in rich
abundance into one that has become depleted by the excessive
population. Here is natural selection at the enzyme level. As each
precursor becomes limiting, there is a selection pressure favoring any
enzyme that can synthesize the molecule in short supply. Eventually
the metabolic systems of living things might be built up this way
until a completely autotrophic, photoynthesizing plant comes into
being-- _provided that there will be genes and their enzymes for the
selection process to act upon._
Say that the gene comes into being by mutations consisting of random
rearrangements in the nucleotide chains, as suggested by Neodarwinism.
What are the chances that a suitable gene can be produced? Imagine a
primeval ocean uniformly 2 km deep over the entire earth, containing
DNA molecules at a concentration of about 0.001 M (about 700 grams of
DNA per liter of ocean water). Each double-stranded DNA molecule has
1,000 nucleotide pairs and reproduces itself one million times per
second. Each time it reproduces, it mutates by changing one
nucleotide pair in the sequence. To make the calculation easier,
we'll assume that no two DNA molecules are ever alike. In four
billion years, 7.74 x 10^84 different kinds of DNA molecules will be
produced. These are not nearly enough, so we will allow it to happen
on 10^20 similar planets, producing 7.74 x 10^84 (say 10^85) different
molecules. If we are trying to get one DNA molecule for natural
selection to act upon-- and only one will be suitable-- then the
chances of producing it under these conditions are 10^85/10^600, or 1
in 10^515. Say instead that 10^100 different kinds of molecules would
each be suitable for our act of natural selection. Still only one
molecule out of every 10^500 would be acceptable; and, after four
billion years on 10^20 planets, 10^415 of the first 10^500
possibilities remain to be synthesized. So the chances are still
unimaginably small that a proper DNA molecule will appear-- and if it
does, the problem comes up again the next time a precursor becomes
limiting!
How can we solve the problem? We can reduce its magnitude, perhaps,
but only because I may have exaggerated things in the above example.
It may be that some enzymes require 300 amino acids, all arranged in a
specific order if they are to be active, but we don't really know of
any good examples-- which isn't saying much, considering how little we
know about enzyme activity and the arrangement of amino acids. If
most of the amino acids in an enzyme were superfluous-- that is, if
only a few of the amino acids actually were necessary for the active
site-- then the problem might be easier to deal with. Henry Quastler
(1964), in worrying about these matters, calculated that the active
site might require only two amino acids and that seven amino acids
should be sufficient in any case. If only two amino acids are
required, then one out of every 400 combinations ought to be suitable
for any reaction; if seven, then one out of every billion. If this
were true, then the gene is not so unique after all, and random
mutations might be an adequate mechanism.
This answer seems too simple. If only two amino acids produce an
active site, there can only be 400 kinds of active sites, and every
protein would be covered by many, if not most, of them. But enzymes
are highly specific, containing as a rule only one active site. This
suggests that most amino acid sequences are without catalytic
activity. If only a small percentage of amino acid sequences are
active, although there is a legion of active sites (implied by all the
reactions in the myriad life forms), then the number of amino acids in
the minimal sequence must be quite high-- perhaps 15 or 16. Actually,
we have determined the structure of a few enzymes, and it does not
appear that the sequence numbers for an active site are small. In
lysozyme, for example, the substrate binds to the enzyme through at
least six hydrogen bonds and more than 40 somewhat weaker contacts
(Chipman and Sharon, 1969). Because there is much to learn about
enzymes, this is probably the best area to watch for a solution to my
doubts. So far, however, the enzyme chemist has not provided us with
much comforting information.
Religious Convictions Aside...
We are entitled to think about another solution: an intelligent
Creator of life. We can try to write Shakespeare by piling computers
on top of each other and letting them rearrange letters of the
language, but a much better way is to let Shakespeare apply his
intelligence to the job. Could God apply his intelligence to the
ordering of nucleotides in DNA chains, providing the genes for
selection to act upon? Certainly, if He exists. I believe in such a
God for reasons quite independent of the discussion here. But
scientifically this solution is not satisfying, because it does not
(to me, at least) suggest reasonable scientific tests; indeed, it
might even lead to a complacent loss of desire to use science in the
first place. The idea may be an important part of my personal life,
but so far I see no suitable way to make it a part of my scientific
life.
Perhaps the mutations upon which natural selection acts are not really
random at all. Perhaps there is some feedback from the environment to
enzymes and genes, directing the mutation process. Here at least is
an idea that might be tested.
Questions About Mutation
An argument that I encounter is that the theory of mutations has been
demonstrated, so my doubts are in vain. I am not convinced. Most
textbooks (for example, Stebbins, 1966) suggest that, while the vast
majority of mutations may be bad, some are good-- perhaps "one in a
thousand." The number is pretty much a wild guess, but there are some
experimental data suggesting that it could be close. Apparently
potentially adaptive ("good") mutations have appeared after
irradiating corn or some microorganism. Still I'm not convinced. My
doubts are confined to occasions when we must produce a gene _de
novo_, as in the example given above. This gene had to have certain
capabilities because a certain precursor was limiting. In many other
cases, genes might arise by slight changes in preexisting genes,
improving slightly the activity of the controlled enzyme. This could
account for a lot of apparently good mutations that don't fit my
example. Or perhaps a good gene has mutated to become deleterious.
It might mutate back to the original, producing an apparently good
mutation.
Most examples cited to prove the modern synthetic theory of evolution
don't depend upon mutations at all. The peppered moths of England are
often mentioned. Before the Industrial Revolution, most were a
mottled gray color similar to the lichen-covered bark of English
trees. As these trees became covered with soot, the moths became
black-- a protective coloration against predators. This is a
marvelous example of a change in population gene frequency in response
to selection pressures, but the black moths were known to be present
before the Industrial Revolution (albeit in very small numbers). Nor
am I convinced by the oft-cited answers to the work of Wilhelm
Johanssen (1903). Johanssen's bean plants were not changed by
selection after the first few generations, but the protein and oil
contents of corn plants were changed for many generations (Hopkins,
1899). This says nothing about mutations for protein and oil content.
It merely says that the bean plants had already been highly selected
before Johanssen used them and that the corn plants had not been so
selected. It also says that protein and oil contents may depend upon
a large number of genes and that many generations are required to
"collect" these in single individuals. It is a fine demonstration of
selection changing gene frequencies, but it has nothing to do with the
question that bothers me.
Some Further Doubts
Doubting can get to be a bit of a habit-- as it should be with more
students of science. I feel that the doubts expressed above are based
on solid grounds, but I have other doubts remaining more at the
intuitive level. Here are a few, for what they are worth:
Surely our ideas about the origin of life will have to change
radically with the passage of time. Not only is the gene itself a
problem: think of the systems that would have to come into being to
produce a living cell! It's nice to talk about replicating DNA
molecules arising in the soupy sea, but in modern cells this
replication requires the presence of suitable enzymes. Furthermore,
DNA by itself accomplishes nothing. Its only reason for existence is
the information that it carries and that is used in the production of
a protein enzyme. At the moment, the link between DNA and the enzyme
is a highly complex one, involving RNA and an enzyme for its synthesis
on a DNA template; ribosomes; enzymes to activate amino acids; and
transfer-RNA molecules. Yet selection acts only upon phenotypes and
not upon genes. At this level, the phenotype is the enzyme itself.
How, in the absence of the final enzyme, could selection act upon DNA
and all the mechanisms for replicating it? It's as though everything
must happen at once: the entire system must come into being as one
unit, or it is worthless. There may well be ways out of this dilemma,
but I don't see them at the moment.
Some enzymes are known to be incredibly complex. Phosphofructokinase
in glycolysis is promoted by ADP and inhibited by citrate and ATP--
even though ATP is a normal substrate. These inhibitions and
promotions accurately regulate the rate of glycolysis in relation to
oxygen concentrations. They do so because of secondary (allosteric)
sites on the enzyme that influence the primary active site. This is
pretty fancy engineering.
Consider something as complex as the photosynthetic apparatus. We can
shine light on a mixture of chlorophyll, water, and carbon dioxide to
our heart's content, but nothing happens. We need chlorophyll
attached to a suitable protein in a granum embedded in the stroma and
with all the necessary enzymes for the entire photosynthetic process.
Are there halfway steps along the way to this, each with a selective
value of its own? This is the restriction that Darwinism and
Neodarwinism place upon us. No step in evolution can last unless it
has value.
And how many times in our evolution of photosynthesis, respiration,
etc., do we encounter the problem of a required enzyme, that does not
exist at all, as in the example above? How many shiny new genes are
required to produce the phloem transport system or a wing or an eye?
Are there really intermediate steps with selection value along the way
to these final forms?
Organisms are _really_ complex. Counting the number of nucleotide
pairs, the nucleus of a man contains about 10^9 bits of genetic
information. Written in normal-sized type, this would fill about
1,000 normal-sized, bound volumes. We are learning that much of the
genetic information in a nucleus is redundant (repeated). If 90% is
redundant, then the "formula of a man" could be written in 100
volumes. Could we really write those 100 volumes in a mere four
billion years by rearranging nucleotides and selecting? Peas are
apparently even more complex than men. They have 10^11 information
bits per nucleus. Perhaps this is because they are nutritionally much
more complex; they must synthesize their own basic foodstuffs from
water, carbon dioxide, minerals, and the energy of light. But the
really complex production of life is the human brain. Will
Neodarwinism account for its origins?
My last doubt concerns so-called parallel evolution. In the
angiosperms the same features of flower structure have apparently
appeared independently several times in unrelated evolutionary lines.
Indeed, the problem is so severe that no satisfactory classification
scheme for flowering plants has yet been devised. Even something as
complex as the eye has appeared several times; for example, in the
squid, the vertebrates, and the arthropods. It's bad enough
accounting for the origin of such things once, but the thought of
producing them several times according to the modern synthetic theory
makes my head swim.
So there are my doubts. Shoot me down if you can.
REFERENCES
CHIPMAN, D. M., and N. SHARON. 1969. Mechanism of lysozyme action.
_Science_ 165: 454-465.
HOPKINS, C. G. 1899. Improvement in the chemical content of the corn
kernel. _Illinois Agricultural Experiment Station Bulletin_ 55.
HOROWITZ, N. H. 1945. On the evolution of biochemical syntheses.
_Proceedings of the National Academy of Science_ 31: 153-157.
JOHANNSEN, W. 1903. _Ober Erblichkeit in Populationen und in reinen
Linien._ Gustav Fischer Verlag, Jena.
QUASTLER, H. 1964. _The emergence of biological organization._ Yale
University Press, New Haven, Conn.
SALISBURY, F. B. 1969. Natural selection and the complexity of the
gene. _Nature_ 224: 342-343.
SMITH, J. M. 1969. Natural selection and the concept of a protein
space. _Nature_ 225: 563-564.
SPETNER, L. M. 1970. Natural selection versus gene uniqueness.
_Nature_ 226: 948-949.
STEBBINS, G. L. 1966. _Processes of organic evolution._
Prentice-Hall, Inc., Englewood Cliffs, N.J.
=========================================================
For Further Reading
"It's bad enough accounting for the origin of such things [flower
structures, eyes] once, but the thought of producing them several
times according to the modern synthetic theory makes my head swim."
accounting for parallel and convergent supposed-blindwatchmaking
http://www.google.com/groups?selm=Pine.SGI.3.96A.990712220140.883597C-100000%40umbc9.umbc.edu
"But the really complex production of life is the human brain. Will
Neodarwinism account for its origins?"
highly-advanced 'computer' found in nature; Benyus; Tomlin
http://www.google.com/groups?selm=Pine.SGI.4.10A.B3.9911172232160.1113971-100000%40umbc8.umbc.edu
"The modern theory emphasizes the importance of genetic recombinations
but ultimately rests upon mutations as the source of the variability
acted upon by natural selection."
NIEH
http://www.google.com/groups?selm=Pine.SGI.3.96.980604010337.18472C-100000%40umbc9.umbc.edu
Koestler, Waddington, Dobzhansky, and a remark for Gould
http://www.google.com/groups?selm=Pine.SGI.3.96.980606011626.8316A-100000%40umbc8.umbc.edu
"The peppered moths of England are often mentioned."
1922 Bateson, Gould on the major synthesists, Saunders & Ho
http://www.google.com/groups?selm=Pine.SGI.3.96A.990131235540.126906A-100000%40umbc8.umbc.edu
Coyne: classic peppered moth story "is in bad shape, and, while not
yet ready for the glue factory, needs serious attention"
http://www.google.com/groups?selm=b1c67abe.0402230510.519fe8a1%40posting.google.com
Coyne and Feynman on Santa Claus
http://www.google.com/groups?selm=Pine.SGI.3.96A.981124234529.22878A-100000%40umbc8.umbc.edu
"Choosing from these characters, we can write the following sentence
from Shakespeare"
Sean P. (a creationist) on Dawkins's "Methinks it is like a weasel"
illustration
http://www.google.com/groups?selm=b1c67abe.0401142214.3c4c92b0%40posting.google.com
"If only a small percentage of amino acid sequences are active"
# of functional amino acid sequences?
http://www.google.com/groups?selm=Pine.SGI.3.96A.990425235307.3226566A-100000%40umbc9.umbc.edu
Sean P. (a creationist) on amino acid sequences
http://www.google.com/groups?selm=80d0c26f.0401040827.4811a655%40posting.google.com
http://www.google.com/groups?selm=80d0c26f.0312211829.68031aac%40posting.google.com
http://www.google.com/groups?selm=80d0c26f.0312301019.6875127a%40posting.google.com
http://www.google.com/groups?selm=80d0c26f.0312181225.4c095dcd%40posting.google.com
"Now we know that the cell itself is far more complex than we had
imagined."
1921 Kostychev in
The Search for a Loophole to the Beginning of the Universe
in the Big Bang and to the Seeming-Design of Physics
http://www.google.com/groups?selm=Pine.LNX.4.10A.B3.10005292327160.25513-100000%40jabba.gl.umbc.edu
"Furthermore, the most primitive ones [forms of life] existed at [the]
earliest times, the most complex ones most recently."
Compare
views of Cuvier, d'Orbigny, and Agassiz (all creationists)
http://www.google.com/groups?selm=Pine.SGI.3.96A.980819011221.8126B-100000%40umbc9.umbc.edu
"This is pretty fancy engineering."
Compare
Julie T. (a creationist) on Examples of Bioengineering
http://www.google.com/groups?selm=Pine.SGI.3.96A.990809215054.1512874F-100000%40umbc9.umbc.edu
"this solution ["an intelligent Creator of life"] is not satisfying,
because it does not (to me, at least) suggest reasonable scientific
tests"
Compare
Julie T. on biological design
http://www.google.com/groups?selm=Pine.SGI.4.44L.01.0307231113280.765971-100000%40irix2.gl.umbc.edu
raven1
ford) wrote:
>Salisbury, Frank B. September 1971. "Doubts About the Modern
>Synthetic Theory of Evolution" _The American Biology Teacher_,
>335-338, 354.
This would be funny if it weren't so sad. Posting it in the first
place falls into the category of the fallacy of Invalid Appeal to
Authority, second, the article itself is primarily composed of the
fallacies of Argument from Personal Incredulity and Argument from
Ignorance.
"Rev Dr" Lenny Flank
david ford wrote:
> Salisbury, Frank B. September 1971. "Doubts About the Modern
> Synthetic Theory of Evolution" _The American Biology Teacher_,
> 335-338, 354.
>
How dreadful. For some odd reason, though, you neglect to mention that
he thinks creationists are kooks, just like Behe does.
What, if anything, is the scientific theory of creation. How, if any
way, can we test it using the scientific method?
Is there some sort of problem with your answering that simple question,
David?
===============================================
Lenny Flank
"There are no loose threads in the web of life"
Creation "Science" Debunked:
http://www.geocities.com/lflank
DebunkCreation Email list:
http://www.groups.yahoo.com/group/DebunkCreation
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johac
dfo...@gl.umbc.edu (david ford) wrote:
> Salisbury, Frank B. September 1971. "Doubts About the Modern
> Synthetic Theory of Evolution" _The American Biology Teacher_,
> 335-338, 354.
>
1971? Don't you have anything a little more recent? We have done some
scince in the past 33 years, you know.
--
John Hachmann aa #1782
"Men become civilized not in their willingness to believe, bit in
proportion to their readiness to doubt." - H. L. Mencken
johac
raven1 <quotht...@nevermore.com> wrote:
And not to mention that most of what is in there is badly outdated.
"Rev Dr" Lenny Flank
johac wrote:
> In article <b1c67abe.04022...@posting.google.com>,
> dfo...@gl.umbc.edu (david ford) wrote:
>
>
>>Salisbury, Frank B. September 1971. "Doubts About the Modern
>>Synthetic Theory of Evolution" _The American Biology Teacher_,
>>335-338, 354.
>>
>
> 1971? Don't you have anything a little more recent? We have done some
> scince in the past 33 years, you know.
Not creationists. They haven't come up with a new argument sicne Morris
wrote "The Genesis Flood" back in the early 60's (hell, not sicne
McReady Price wrote his books back in the 1920's).
david ford
> In article <b1c67abe.04022...@posting.google.com>,
> dfo...@gl.umbc.edu (david ford) wrote:
>
> > Salisbury, Frank B. September 1971. "Doubts About the Modern
> > Synthetic Theory of Evolution" _The American Biology Teacher_,
> > 335-338, 354.
>
> 1971? Don't you have anything a little more recent?
Yes, and yes.
> We have done some
> scince in the past 33 years, you know.
Noooo. Get out of here!
Ummm, has this [j]"scince in the past 33 years" decisively laid to
rest the basis for Salisbury's doubts?
david ford
What's an [r]"Invalid Appeal to Authority"?
Is there such a thing as a "Valid Appeal to Authority"?
Is there such a thing as an "Argument from Collective Incredulity"?
What's an [r]"Argument from Personal Incredulity"?
Suppose someone says "I've heard what you have to say, and I don't
accept your claim that X occurred [or: didn't occur]-- your evidence
and arguments simply are not persuasive to me." Does this statement
invoke an [r]"Argument from Personal Incredulity"?
What's an [r]"Argument from Ignorance"?
Suppose someone says, "Here's a list of over 100 organs and body
structures that have no known function. These organs and body
structures are function-less." Is that person making an [r]"Argument
from Ignorance"?
johac
dfo...@gl.umbc.edu (david ford) wrote:
> johac <jha...@ixpresremove.com> wrote in message
> news:<jhachm-B1E8E4....@news-60.giganews.com>...
> > In article <b1c67abe.04022...@posting.google.com>,
> > dfo...@gl.umbc.edu (david ford) wrote:
> >
> > > Salisbury, Frank B. September 1971. "Doubts About the Modern
> > > Synthetic Theory of Evolution" _The American Biology Teacher_,
> > > 335-338, 354.
> >
> > 1971? Don't you have anything a little more recent?
>
> Yes, and yes.
>
> > We have done some
> > scince in the past 33 years, you know.
>
> Noooo. Get out of here!
> Ummm, has this [j]"scince in the past 33 years" decisively laid to
> rest the basis for Salisbury's doubts?
>
Why don't you ask a scientist? Or go to a library and look up some peer
reviewed scientific journals. Let us know how many articles on evolution
you find and how many on creationism or intelligent design.
--
John Hachmann aa #1782
"Men become civilized not in their willingness to believe, but in
Danny Kodicek
"david ford" <dfo...@gl.umbc.edu> wrote in message
news:b1c67abe.04022...@posting.google.com...
> Salisbury, Frank B. September 1971. "Doubts About the Modern
> Synthetic Theory of Evolution" _The American Biology Teacher_,
> 335-338, 354.
To be fair, this is a much better piece than David's general quotemine
standard. The question of generation of variation I think remains an
interesting one and one which still deserves thought. In fact, I've been
thinking recently that in some ways it provides the dividing line between
those awkward terms of micro and macroevolution. In a nutshell,
microevolution could be described as the selection of particular existing
alleles from the gene pool, while macroevolution would be the coming into
being of new alleles or gene sites. By this definition, it's not surprising
that microevolution occurs rapidly to adapt to novel environments, because
selection occurs in the space of a small number of generations. One would
expect that in usual circumstances, with a large gene pool and a
slowly-changing environment, microevolution would work so much faster than
its macro-cousin that it would be very hard for new genetic material to get
a foothold. Only when a population is isolated, decreasing the gene pool, or
when the environment changes particularly quickly and the existing gene pool
can't adapt, would you expect macroevolution to make a difference, and this
is where we get speciation.
This is just an aside - it's something I found myself musing on at a spare
moment recently, and it's probably old hat anyway.
To return to the subject at hand, there's nothing in the theory of Natural
Selection which *intrinsically* requires that variation has to be random. It
does predict that random variation is sufficient, along with selection, to
create complexity, but that doesn't mean that there can't be directed
variation too. Variation might be directed, for example, by processes like
self-catalysis, or 'quantum evolution', which I was reading about a while
ago. For that matter, it could proceed by Lamarckian processes (the fact
that it doesn't on this planet doesn't mean it's not possible - after all,
evolution in the world of memes rather than genes is Lamarckian).
So just because this piece was posted by David doesn't necessarily mean it's
stupid. And indeed, it specifically refutes David's belief in creation and
intelligent design.
Danny
Stanley Friesen
>What's an [r]"Argument from Personal Incredulity"?
An argument based on the premise that if *I* can't imagine it, it could
not possibly be real.
>Suppose someone says "I've heard what you have to say, and I don't
>accept your claim that X occurred [or: didn't occur]-- your evidence
>and arguments simply are not persuasive to me." Does this statement
>invoke an [r]"Argument from Personal Incredulity"?
No, as it makes no claims about reality, only about your personal
beliefs.
>
>What's an [r]"Argument from Ignorance"?
>Suppose someone says, "Here's a list of over 100 organs and body
>structures that have no known function. These organs and body
>structures are function-less." Is that person making an [r]"Argument
>from Ignorance"?
Not really.
The peace of God be with you.
Stanley Friesen
david ford
david ford:
johac:
david ford:
> > > > Salisbury, Frank B. September 1971. "Doubts About the Modern
> > > > Synthetic Theory of Evolution" _The American Biology Teacher_,
> > > > 335-338, 354.
> > >
> > > 1971? Don't you have anything a little more recent?
> >
> > Yes, and yes.
> >
> > > We have done some
> > > scince in the past 33 years, you know.
> >
> > Noooo. Get out of here!
> > Ummm, has this [j]"scince in the past 33 years" decisively laid to
> > rest the basis for Salisbury's doubts?
>
> Why don't you ask a scientist?
I have spotted a few scientists in these newsgroups.
They know they are more than welcome to respond.
As are you.
> Or go to a library and look up some peer
> reviewed scientific journals.
Which, if any, articles did you have in mind?
I hope it is not the case that you have this vague feeling that
Salisbury's doubts have been decisively laid to rest, and assert to me
that such has been done, even as you lack good grounds for saying such
occurred.
> Let us know how many articles on evolution
> you find and how many on creationism or intelligent design.
You didn't answer my question.
You earlier asked if I had [j]"anything a little more recent" than
1971 Salisbury. Some support for my "yes" response appears in this
collection of my posts:
http://www.google.com/groups?selm=b1c67abe.0402272033.14eb36f2%40posting.google.com
Tracy Hamilton
A WHOLE lot more is know about mutations, and their effects on
phenotype since 1971.
Does NeoDarwinism include neutral evolution?
> First, let me emphasize that it is quite foolish to doubt most of the
> evolutionary story. The fossils are there, and their mute testimony
> is overwhelming evidence that numerous forms of life have existed on
> earth over immense spans of time. Furthermore, the most primitive
> ones existed at [the] earliest times, the most complex ones most
> recently. Fundamentalist writers and others have tried to provide
> reasonable alternative explanations for the fossils, but these are
> never convincing. Furthermore, the mechanism of natural selection as
> described by Darwin and the modern embellishments upon it provided by
> population geneticists can hardly be questioned. Gene frequencies do
> change in populations as a result of selection pressures. This has
> been observed in the field and duplicated in the laboratory. No
> scientific fact could be demonstrated more clearly.
[snip]
> One might begin (as I did) to get the intuitive feeling that genes and
> enzymes are too complex to originate by randomly changing nucleotide
> sequences. But intuitive feelings are often wrong and never really
> satisfying. How can we pin it down?
>
> How Many Genes Could Exist?
A whole bunch.
What about how many genes could *work*? Would they be generated
randomly - a relevant question because the deleted calculations were
done assuming independence of probability of a configuration from its
makeup.
Another question - what do genes have to do with abiogenesis?
In the RNA world, you have no DNA. Maybe that is a crucial
factor in why taking 1971 ideas uncritically is laughable. Have
you been asleep for 20 years?
[snip]
> So the chances are still
> unimaginably small that a proper DNA molecule will appear-- and if it
> does, the problem comes up again the next time a precursor becomes
> limiting!
[snip]
Tracy P. Hamilton
johac
dfo...@gl.umbc.edu (david ford) wrote:
Well, I got about as far as his discussion on genes and the number of
them. Looking back at 1971, when I was starting out in molecular
biology, we knew a few things about genes, but relatively little about
their structure or how they worked. Look at how much we have learned
since. We have sequenced the human genome. We have approximately
30-40,000 genes. For more information and many references, see the
Genome Project website:
By sequencing the genomes of other organisms and comparing them we have
learned much not only about the organization and structure of genes, but
valuable insights as to how they evolved, and what mutations occurred
along the way. And most of the work was done in the last four or five
years!
I also found his treatment of mutations very weak. We know mutations
occur, we can detect them and measure their frequency. We can
artificially induce mutations in genes and study their effects. I would
do a Google search for "mutagenesis"
As far as mutation and evolution, a good discussion is at:
http://www.talkorigins.org/faqs/fitness/
For more references, I have too many to paste in, but try:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
Type in 'mutation' or whatever you want. Most of the articles are by
subscription, so you will need to go to a library to look them up.
Reading further into the article I found the old creationist mistake of
confounding abiogenesis (origin of life) with evolution. They are
separate phenomena.
To make matters worse, he frequently uses the familiar argument from
ignorance: "If science can't explain something today, it must be a
god's/intelligent designer's doing". This is also known as the "god of
the gaps" argument. Using my example of the genome project above, see
how much we have learned in the last few years. The gaps are getting
smaller.
I haven't read through the entire article yet, but I will comment on it
if I find anything significant.
>
> > Let us know how many articles on evolution
> > you find and how many on creationism or intelligent design.
>
> You didn't answer my question.
> You earlier asked if I had [j]"anything a little more recent" than
> 1971 Salisbury. Some support for my "yes" response appears in this
> collection of my posts:
> http://www.google.com/groups?selm=b1c67abe.0402272033.14eb36f2%40posting.googl
> e.com
Thanks for the references, I'll take a look at them when I get some time.
Richard S. Crawford
> dfo...@gl.umbc.edu (david ford) wrote :
>
>
>>I have spotted a few scientists in these newsgroups.
>>They know they are more than welcome to respond.
>
>
> I do now: I am the head of Creation Science at Broomleigh Baptist Church.
No, no. David said "Scientist". Not "fruitcake who doesn't have a clue
what science is or what scientists do and in poisoning our children with
their dogmatic anti-science crap while pushing a dangerous political
agenda."
John Monrad
article <c2acia$kob$1...@woodrow.ucdavis.edu>...
Check out the link Elder Exford provided. Closely.
--
John Monrad
Richard S. Crawford
Oh. My bad. I'll go find a hole to hide in for awhile.
(Goes to show, though, how I've learned from Creationists: don't read
the links provided by the opposition, just assume they're wrong and
trumble forth like an annoying bulldozer.)
Apologies to Elder Exford.
david ford
david ford in message
news:b1c67abe.04022...@posting.google.com...
> > Salisbury, Frank B. September 1971. "Doubts About the Modern
> > Synthetic Theory of Evolution" _The American Biology Teacher_,
> > 335-338, 354.
> >
> > The problem is the origin of variability. Both Lamarck and De Vries
> > put forth their theories to account for this. Darwin was fully aware
> > of the seriousness of the problem, and he retreated with misgivings to
> > Lamarck's ideas. The modern theory emphasizes the importance of
> > genetic recombinations but ultimately rests upon mutations as the
> > source of the variability acted upon by natural selection. This is
> > where I run into problems.
>
> A WHOLE lot more is know about mutations, and their effects on
> phenotype since 1971.
Splendid. Then you should have no problem listing a mere 20 of the
better mutations plausibly characterized as mutations that can lead to
the appearance in phenotypes of new organs & new structures having new
functions. A talk.origins FAQ might be able to assist with
presentation of the list.
> Does NeoDarwinism include neutral evolution?
Yes. And no. "Neo-Darwinism" is rather vague, and can include or not
include [TH]"neutral evolution" depending on who is advancing
neo-Darwinism, when, and how.
> > First, let me emphasize that it is quite foolish to doubt most of the
> > evolutionary story. The fossils are there, and their mute testimony
> > is overwhelming evidence that numerous forms of life have existed on
> > earth over immense spans of time. Furthermore, the most primitive
> > ones existed at [the] earliest times, the most complex ones most
> > recently. Fundamentalist writers and others have tried to provide
> > reasonable alternative explanations for the fossils, but these are
> > never convincing. Furthermore, the mechanism of natural selection as
> > described by Darwin and the modern embellishments upon it provided by
> > population geneticists can hardly be questioned. Gene frequencies do
> > change in populations as a result of selection pressures. This has
> > been observed in the field and duplicated in the laboratory. No
> > scientific fact could be demonstrated more clearly.
>
> [snip]
>
> > One might begin (as I did) to get the intuitive feeling that genes and
> > enzymes are too complex to originate by randomly changing nucleotide
> > sequences. But intuitive feelings are often wrong and never really
> > satisfying. How can we pin it down?
> >
> > How Many Genes Could Exist?
>
> A whole bunch.
> What about how many genes could *work*?
Question: How many possible combinations of letters, spaces, and
punctuation marks of length N could exist?
Answer: A whole bunch.
Question: How many of these combinations would be intelligible in
English?
Answer: Far, far, _far_ fewer than the number of possible
combinations.
I'm re-inserting some URLs that suffered snippage.
"If only a small percentage of amino acid sequences are active"
# of functional amino acid sequences?
http://www.google.com/groups?selm=Pine.SGI.3.96A.990425235307.3226566A-100000%40umbc9.umbc.edu
Sean P. (a creationist) on amino acid sequences
http://www.google.com/groups?selm=80d0c26f.0401040827.4811a655%40posting.google.com
http://www.google.com/groups?selm=80d0c26f.0312211829.68031aac%40posting.google.com
http://www.google.com/groups?selm=80d0c26f.0312301019.6875127a%40posting.google.com
http://www.google.com/groups?selm=80d0c26f.0312181225.4c095dcd%40posting.google.com
> Would they be generated
> randomly - a relevant question because the deleted calculations were
> done assuming independence of probability of a configuration from its
> makeup.
Mutations are said to occur randomly, so yes, the gene sequences would
be generated randomly. I do not know what you mean by [TH]"assuming
independence of probability of a configuration from its makeup."
> Another question - what do genes have to do with abiogenesis?
> In the RNA world, you have no DNA. Maybe that is a crucial
> factor in why taking 1971 ideas uncritically is laughable. Have
> you been asleep for 20 years?
One could replace Salisbury's "DNA" with "RNA" without appreciably
changing his arguments.
At one point the DNA-RNA-protein system arose. How did it arise?
[TH]"In the RNA world" What is the evidence for the existence at one
time of an RNA world?
Joyce, Wald, Simpson, Dose, about Thaxton
http://www.google.com/groups?selm=Pine.SGI.3.96A.990811214247.4395286C-100000%40umbc9.umbc.edu
1995 Yockey on the Grand Academy of Lagado
http://www.google.com/groups?selm=b1c67abe.0402032212.46bef779%40posting.google.com
Tracy Hamilton
> Tracy Hamilton <DontSpam...@uab.edu> on 3 Mar 2004
> david ford in message
> news:b1c67abe.04022...@posting.google.com...
>
> > > Salisbury, Frank B. September 1971. "Doubts About the Modern
> > > Synthetic Theory of Evolution" _The American Biology Teacher_,
> > > 335-338, 354.
> > >
> > > The problem is the origin of variability. Both Lamarck and De Vries
> > > put forth their theories to account for this. Darwin was fully aware
> > > of the seriousness of the problem, and he retreated with misgivings to
> > > Lamarck's ideas. The modern theory emphasizes the importance of
> > > genetic recombinations but ultimately rests upon mutations as the
> > > source of the variability acted upon by natural selection. This is
> > > where I run into problems.
> >
> > A WHOLE lot more is know about mutations, and their effects on
> > phenotype since 1971.
>
> Splendid. Then you should have no problem listing a mere 20 of the
> better mutations plausibly characterized as mutations that can lead to
> the appearance in phenotypes of new organs & new structures having new
> functions. A talk.origins FAQ might be able to assist with
> presentation of the list.
You didn't seem to understand the point. It is about all the different
kinds of
things that lead to significant change. First of all, not all mutations are
point mutations. For example, transposons were not generally
realized for how important they are, which is why Barbara McClintock
did not get the Nobel prize until 12 years after Salisbury's article.
Second, there are genes whose effects on phenotype are major (HOX
genes, discovered first 7 years after Salisbury's article), with rather
significant differences arising in phenotype just from changing
timing or expression quantities, or rather subtle changes. It all
depends on what changes. This is directly related to somebodies
(Salisbury in this case) doubts about whether mutations can cause
*enough* change.
Third, what is meant by a new organ? Is a dog's paw and my hand
two of the same thing, or two new structures? Is a new enzyme
a new structure - ie is structure only cell morphology? Is a breast
a new structure, or just a modified sweat gland?
> > Does NeoDarwinism include neutral evolution?
>
> Yes. And no. "Neo-Darwinism" is rather vague, and can include or not
> include [TH]"neutral evolution" depending on who is advancing
> neo-Darwinism, when, and how.
Since neutral evolution was not generally known *in 1971* by
most biologists, the answer would be *no*. We get enough knuckleheads
*today*, who by their writing can't make it clear that they realize that
there is a
distinction, either through dishonesty or ignorance.
> > > First, let me emphasize that it is quite foolish to doubt most of the
> > > evolutionary story. The fossils are there, and their mute testimony
> > > is overwhelming evidence that numerous forms of life have existed on
> > > earth over immense spans of time. Furthermore, the most primitive
> > > ones existed at [the] earliest times, the most complex ones most
> > > recently. Fundamentalist writers and others have tried to provide
> > > reasonable alternative explanations for the fossils, but these are
> > > never convincing. Furthermore, the mechanism of natural selection as
> > > described by Darwin and the modern embellishments upon it provided by
> > > population geneticists can hardly be questioned. Gene frequencies do
> > > change in populations as a result of selection pressures. This has
> > > been observed in the field and duplicated in the laboratory. No
> > > scientific fact could be demonstrated more clearly.
Well, do you agree with it? There was even enough known back then that
Salisbury could make this statement. NS is not dead. Crusading against
it is foolish.
> > [snip]
> >
> > > One might begin (as I did) to get the intuitive feeling that genes and
> > > enzymes are too complex to originate by randomly changing nucleotide
> > > sequences. But intuitive feelings are often wrong and never really
> > > satisfying. How can we pin it down?
> > >
> > > How Many Genes Could Exist?
> >
> > A whole bunch.
> > What about how many genes could *work*?
>
> Question: How many possible combinations of letters, spaces, and
> punctuation marks of length N could exist?
> Answer: A whole bunch.
> Question: How many of these combinations would be intelligible in
> English?
> Answer: Far, far, _far_ fewer than the number of possible
> combinations.
Language is much more brittle with repect to changes. For example, if one
takes changes of one rather large group of amino acid residues (say polar),
changing one polar residue to a different polar one generally has little
effect on the result.
Can you say that for language? No.
And, is there a difference in the distribution because there is a different
rate at which two sequences of letters get generated? No.
Is much of a sentence only to make sure that a certain word shows
up in a certain position next to another? No.
That you can even entertain such an analogy betrays deep ignorance of the
nature of structure-function relationships in biomolecules.
> I'm re-inserting some URLs that suffered snippage.
> "If only a small percentage of amino acid sequences are active"
How can somebody make a definitive statement that X fraction
of amino acid sequences are "active", when getting the 3-D structure right
for a single, given sequence is at best 50%, much less the functions
that result from that structure.
[snip]
> > Would they be generated
> > randomly - a relevant question because the deleted calculations were
> > done assuming independence of probability of a configuration from its
> > makeup.
>
> Mutations are said to occur randomly, so yes, the gene sequences would
> be generated randomly. I do not know what you mean by [TH]"assuming
> independence of probability of a configuration from its makeup."
Well, in the production of ATCGATCGATCG from a point mutation
of ATCGATCGATCC, is it relevant that there are 4^12 possible
sequences? That particular mutation would be generated "randomly",
but so would mixing up A,T,C,G and picking out a 12-mers. But not
the same likelihood by a LONG shot.
> > Another question - what do genes have to do with abiogenesis?
> > In the RNA world, you have no DNA. Maybe that is a crucial
> > factor in why taking 1971 ideas uncritically is laughable. Have
> > you been asleep for 20 years?
>
> One could replace Salisbury's "DNA" with "RNA" without appreciably
> changing his arguments.
Holy Cow!
> At one point the DNA-RNA-protein system arose. How did it arise?
> [TH]"In the RNA world" What is the evidence for the existence at one
> time of an RNA world?
I think trying to get into this is a bit ambitious, when your questions
betray
a total ignorance of the basics of what we know of current systems.
[snip]
I think maybe a return to understanding (as even Salisbury did)
that natural selection is well established should be done first. If you
can't get that, what point is there to discussing your other
misunderstandings?
What have you done to get even an *elementary* understanding?
How much reading of biochemistry have you done? May I suggest a
college text, perhaps by someone named Larry Moran?
Tracy P. Hamilton
Elder Keith Exford
<rscrawf...@mossREMOVEWATERFOWLroot.com>
wrote:
>> Check out the link Elder Exford provided. Closely.
> Apologies to Elder Exford.
Closely, he said.
Okay, it's my Christian obligation, so I'll forgive you.
God bless, etc.
--
Broomleigh Baptist Church
Creation Science Department
http://exford.broomleigh.org/
david ford
david ford:
Tracy Hamilton on 3 Mar 2004:
david ford:
> > > > Salisbury, Frank B. September 1971. "Doubts About the Modern
> > > > Synthetic Theory of Evolution" _The American Biology Teacher_,
> > > > 335-338, 354.
> > > >
> > > > The problem is the origin of variability. Both Lamarck and De Vries
> > > > put forth their theories to account for this. Darwin was fully aware
> > > > of the seriousness of the problem, and he retreated with misgivings to
> > > > Lamarck's ideas. The modern theory emphasizes the importance of
> > > > genetic recombinations but ultimately rests upon mutations as the
> > > > source of the variability acted upon by natural selection. This is
> > > > where I run into problems.
> > >
> > > A WHOLE lot more is know about mutations, and their effects on
> > > phenotype since 1971.
> >
> > Splendid. Then you should have no problem listing a mere 20 of the
> > better mutations plausibly characterized as mutations that can lead to
> > the appearance in phenotypes of new organs & new structures having new
> > functions. A talk.origins FAQ might be able to assist with
> > presentation of the list.
>
> You didn't seem to understand the point.
An intriguing response. You didn't fulfill the request for
supportive evidence, and then claimed that I don't [TH]"seem
to understand the point."
> It is about all the different
> kinds of things that lead to significant change. First of all,
> not all mutations are point mutations.
I knew that.
> For example, transposons were
> not generally realized for how important they are, which is why
> Barbara McClintock did not get the Nobel prize until 12 years
> after Salisbury's article.
>
> Second, there are genes whose effects on phenotype are major (HOX
> genes, discovered first 7 years after Salisbury's article), with rather
> significant differences arising in phenotype just from changing
> timing or expression quantities, or rather subtle changes.
I was once told that "HOX mutations, as all mutations with
drastic effects, usually lower survival radically"-- would you
agree?
http://www.google.com/groups?selm=Pine.SGI.3.96.980530001102.4784B-100000%40umbc8.umbc.edu
> It all
> depends on what changes. This is directly related to somebodies
> (Salisbury in this case) doubts about whether mutations can cause
> *enough* change.
I'm sure that Salisbury would agree that some mutations
produce _much_ change. However, that massive change is
usually harmful, is practically never helpful, and is
practically never a sort of change that could plausibly be said
to contribute to the appearance of biological novelty.
> Third, what is meant by a new organ?
Better question: What is meant by a new organ or new
structure having a new function?
> Is a dog's paw and my hand
> two of the same thing, or two new structures? Is a new
> enzyme a new structure - ie is structure only cell
> morphology? Is a breast a new structure, or just a modified
> sweat gland?
If a dog with paws transformed into a creature having hands
in place of paws, I'd say the hands were new structures
having new functions.
[TH]"Is a new enzyme a new structure" I'm speaking about
gross morphological changes.
About your last question, if a population of creatures having
sweat glands and no breasts transformed into a population of
creatures in which a proportion of its sweat glands
transformed into breasts, I'd say that the breasts were new
structures having new functions.
I'll ask my question again. Please list a mere 20 of the better
mutations plausibly characterized as mutations that can lead
to the appearance in phenotypes of new organs & new
structures having new functions. A talk.origins FAQ that
might be able to assist with presentation of the list is "Are
Mutations Harmful?"
http://www.talkorigins.org/faqs/mutations.html
> > > Does NeoDarwinism include neutral evolution?
> >
> > Yes. And no. "Neo-Darwinism" is rather vague, and can include or not
> > include [TH]"neutral evolution" depending on who is advancing
> > neo-Darwinism, when, and how.
>
> Since neutral evolution was not generally known *in 1971* by
> most biologists, the answer would be *no*.
What is the answer today, in 2004?
> We get enough knuckleheads
> *today*, who by their writing can't make it clear that they realize that
> there is a distinction, either through dishonesty or ignorance.
>
> > > > First, let me emphasize that it is quite foolish to doubt most of the
> > > > evolutionary story. The fossils are there, and their mute testimony
> > > > is overwhelming evidence that numerous forms of life have existed on
> > > > earth over immense spans of time. Furthermore, the most primitive
> > > > ones existed at [the] earliest times, the most complex ones most
> > > > recently. Fundamentalist writers and others have tried to provide
> > > > reasonable alternative explanations for the fossils, but these are
> > > > never convincing. Furthermore, the mechanism of natural selection as
> > > > described by Darwin and the modern embellishments upon it provided by
> > > > population geneticists can hardly be questioned. Gene frequencies do
> > > > change in populations as a result of selection pressures. This has
> > > > been observed in the field and duplicated in the laboratory. No
> > > > scientific fact could be demonstrated more clearly.
>
> Well, do you agree with it? There was even enough known back then that
> Salisbury could make this statement. NS is not dead. Crusading against
> it is foolish.
I fully agree that [Salisbury]"Gene frequencies do change in
populations as a result of selection pressures." Salisbury
writes immediately following the material you drew attention
to, [Salisbury]"But will changes in gene frequencies in
response to selection pressures account for evolution in the
broadest sense: life.... developing over eons of time until the
earth is covered with flowering plants and thinking men?"
Salisbury strongly suspected "no"-- he had his doubts.
I would reply "no" to Salisbury's question: the
neo-Darwinian conception of natural selection is dead.
Darwin's theory of natural selection is dead. The allegation
that mutation + natural selection can result in the appearance
of new organs and new structures having new functions is
dead.
> > > [snip]
> > >
> > > > One might begin (as I did) to get the intuitive feeling that genes and
> > > > enzymes are too complex to originate by randomly changing nucleotide
> > > > sequences. But intuitive feelings are often wrong and never really
> > > > satisfying. How can we pin it down?
> > > >
> > > > How Many Genes Could Exist?
> > >
> > > A whole bunch.
> > > What about how many genes could *work*?
> >
> > Question: How many possible combinations of letters, spaces, and
> > punctuation marks of length N could exist?
> > Answer: A whole bunch.
> > Question: How many of these combinations would be intelligible in
> > English?
> > Answer: Far, far, _far_ fewer than the number of possible
> > combinations.
>
> Language is much more brittle with repect to changes. For example, if one
> takes changes of one rather large group of amino acid residues (say polar),
> changing one polar residue to a different polar one generally has little
> effect on the result.
> Can you say that for language? No.
Language is much more brittle with repect to changes. For
exampl, if one takes changes ofone rather group large of
aminoacid residues (polar say), changing one polar residue to
a diffrent one polar generally has effect little onthe result.
Can sayyouthat for language?
> And, is there a difference in the distribution because there
> is a different rate at which two sequences of letters get
> generated? No.
Difference in the distribution of what?
> Is much of a sentence only to make sure that a certain word
> shows up in a certain position next to another? No.
Is much of a DNA sequence, RNA sequence, or amino acid
sequence the product of certain nucleotides or amino acids
having to appear next to certain other nucleotides or amino
acids?
> That you can even entertain such an analogy betrays deep ignorance of the
> nature of structure-function relationships in biomolecules.
I had no idea that Hubert Yockey has [TH]"deep ignorance of the
nature of structure-function relationships in biomolecules."
> > I'm re-inserting some URLs that suffered snippage.
> > "If only a small percentage of amino acid sequences are active"
>
> How can somebody make a definitive statement that X fraction
> of amino acid sequences are "active", when getting the 3-D structure right
> for a single, given sequence is at best 50%, much less the functions
> that result from that structure.
It's good to know that I'm conversing with someone that
knows biochemistry. Perhaps you could help answer a
question of mine:
Yockey, Hubert P. "An Application of Information Theory to
the Central Dogma and the Sequence Hypothesis" _Journal
of Theoretical Biology_ 46: 369-406 (1974). On 371:
The vast majority of the sequences in the ensemble of all
sequences of length _N_, of letters of a written language
have no assigned meaning or specificity. The same is
true of sequences of digits zero through nine and of
musical notes. However, embedded in the ensemble of
all such sequences are, say, a play by Sophocles, the lost
works of Aristotle.... By the same token the protein
sequences of length _N_, which carry specificity, are
embedded in the ensemble of all amino acids sequences
of length _N_. Those sequences which carry specificity
are a tiny fraction of the ensemble.
Statement: "Those amino acid sequences of length N=101
thru N=1010 that carry specificity are a tiny fraction of the
ensemble of all amino acid sequences of length N=101 thru
N=1010." Ballpark answers to the questions below would
help me determine the validity of this statement.
Of all possible amino acid sequences of length 101, what
proportion of those sequences will be functional proteins of
some sort? 1/9th? 1 out of every 2,000? 1/10^17th? 1 out
of every 10^24? 1/10^80th? What?
Same question, this time for amino acid sequences
of length 202?
Of length 303?
Of length 404?
Of length 505?
Of length 606?
Of length 707?
Of length 808?
Of length 909?
Of length 1010?
Also, how long is the biggest functional amino acid sequence
of which you're aware?; of all possible amino acid sequences
of that length, what proportion of those sequences will be
functional proteins of some sort?
> [snip]
>
> > > Would they be generated
> > > randomly - a relevant question because the deleted calculations were
> > > done assuming independence of probability of a configuration from its
> > > makeup.
> >
> > Mutations are said to occur randomly, so yes, the gene sequences would
> > be generated randomly. I do not know what you mean by [TH]"assuming
> > independence of probability of a configuration from its makeup."
>
> Well, in the production of ATCGATCGATCG from a point mutation
> of ATCGATCGATCC, is it relevant that there are 4^12 possible
> sequences? That particular mutation would be generated "randomly",
> but so would mixing up A,T,C,G and picking out a 12-mers. But not
> the same likelihood by a LONG shot.
Let's do some calculations. Probability of obtaining the
sequence
ATCGATCGATCG
by randomly changing the sequence
ATCGATCGATCC
using a 12-sided die to determine which position will next be
changed, and a 4-sided die to determine what that position
will be changed into (with a one in four chance that the
nucleotide will be replaced with the same nucleotide as what
was there originally):
(1/12)(1/4)
or 1 in 48
Probability of obtaining the sequence
ATCGATCGATCG
by selecting 12 nucleotides in a row using a 4-sided die (with
one of A, C, T, and G on each of the four sides) to get the
sequence:
(1/4)(1/4)(1/4)(1/4)(1/4)(1/4)(1/4)(1/4)(1/4)(1/4)(1/4)(1/4)
or 1 in 4^12
I'll need some help with this one:
At one point, neither ATCGATCGATCG nor anything
remotely like it existed.
I'll generously start an organism off with
GGGGGGGGGGG.
Probability of obtaining the sequence
ATCGATCGATCG
by randomly changing the sequence
GGGGGGGGGGG
using a 12-sided die to determine which position will next be
changed, and a 4-sided die to determine what that position
will be changed into:
> > > Another question - what do genes have to do with abiogenesis?
> > > In the RNA world, you have no DNA. Maybe that is a crucial
> > > factor in why taking 1971 ideas uncritically is laughable. Have
> > > you been asleep for 20 years?
> >
> > One could replace Salisbury's "DNA" with "RNA" without appreciably
> > changing his arguments.
>
> Holy Cow!
You disagree. Well, perhaps you could point out a couple
places in Salisbury's article where replacing "DNA" with
"RNA" changes the force of a Salisbury argument.
> > At one point the DNA-RNA-protein system arose. How did it arise?
>
> > [TH]"In the RNA world" What is the evidence for the existence at one
> > time of an RNA world?
>
> I think trying to get into this is a bit ambitious, when your questions
> betray a total ignorance of the basics of what we know of current systems.
If you don't know the answer to the question [df]"What is the
evidence for the existence at one time of an RNA world?"
after having brought up the topic of an RNA world, it's
totally OK to reply that you don't know the answer.
I find it humorous that instead of supplying the requested
evidence or acknowledging not having the requested
evidence, you replied as you did.
I'll ask the other individuals reading this post my questions:
1. At one point the DNA-RNA-protein system arose. How
did it arise?
2. What is the evidence for the existence at one time of an
RNA world?
Davies, Paul. 1999. _The Fifth Miracle: The Search for the
Origin and Meaning of Life_ (New York: Simon &
Schuster), 304pp. Paragraphs on 130-132:
Promising though the RNA-world scenario seems, it has
many detractors. They point out that, however good the
theory may be, test-tube experiments are frequently
dismal failures. Key reactions stubbornly refuse to
proceed without carefully designed procedures and the
help of special catalysts. Nucleic-acid chains are
notoriously fragile, and tend to snap long before they
have acquired the fifty or so base pairs needed for them
to act as enzymes. Water attacks and breaks up
nucleic-acid polymers as it does peptides, casting doubt
on any soupy version of an RNA world. Even the
synthesis of the four bases required as building blocks is
not without serious problems. As far as biochemists can
see, it is a long and difficult road to produce efficient
RNA replicators from scratch. No doubt a way could
eventually be found for each step in the chemical
sequence to be carried out in the lab without too much
drama, but only under highly artificial conditions, using
specially prepared and purified chemicals in just the
right proportions. The trouble is, there are very many
such steps involved, and each requires different special
conditions. It is highly doubtful that all these steps
would obligingly happen one after the other "in the
wild," where a chemical soup or scum would just have
to take pot luck.
The conclusion has to be that, without a trained organic
chemist on hand to supervise, nature would be
struggling to make RNA from a dilute soup under any
plausible prebiotic conditions. So, although an RNA
world could conceivably function and evolve towards
life if handed to us on a plate (perhaps in a soup bowl
would be a better metaphor), getting the RNA world
going from a crude chemical mixture is another matter
entirely.
Added to these diverse difficulties is the problem of
chirality-- left versus right-- that I mentioned in chapter
3. That all life on Earth is based on molecules with the
same chirality is not merely a curiosity: RNA
replication would be menaced in an environment in
which both left- and right-handed versions of the basic
molecules were equally present. The crucial
lock-and-key templating arrangements, whereby bases
pair up with complementary bases according to their
shapes, would be compromised as molecules with the
"wrong" handedness locked into the slots. The left hand
would mess up what the right hand was doing. Unless a
way could be found for nature to create a soup with
molecules of only one handedness, spontaneous RNA
synthesis would be a lost cause.
....
There has also been criticism on theoretical grounds.
The RNA-world theory focuses exclusively on
replication at the expense of metabolism. As I have
stressed already, life is about more than raw
reproduction: living organisms also do things, and must
do them if they are to survive to reproduce. Doing
things costs energy. There has to be a ready source of
energy for organisms to metabolize. In test-tube
experiments, RNA molecules are lovingly supplied with
specialized energetic chemicals to power their activities;
in nature, RNA would have to make do with whatever
was lying around. No Miller-Urey type of experiment
has succeeded in fabricating the energizing chemicals
used by extant life: they are all manufactured inside
cells. Spoon-fed RNA may be a slick replicator, but
without an energy-liberating metabolic cycle already in
place, these fecund molecular strands would soon
become genetic dropouts.
> [snip]
>
> I think maybe a return to understanding (as even Salisbury did)
> that natural selection is well established should be done first. If you
> can't get that, what point is there to discussing your other
> misunderstandings?
Sounds like you're laying the pretext for bowing out of
continuing this discussion. Perhaps the kitchen is getting a
mite too warm.
C. Thompson
Here, in a few short lines, is intellectual dishonesty honed to an art form.
This is the Ming vase of dishonesty. The Waterford crystal. The Tiffany
glass.
Notice where David Ford states:
> I was once told that "HOX mutations, as all mutations with
> drastic effects, usually lower survival radically"-- would you
> agree?
Barely 20 lines later, he repeats this request:
> I'll ask my question again. Please list a mere 20 of the better
> mutations plausibly characterized as mutations that can lead
> to the appearance in phenotypes of new organs & new
> structures having new functions.
David Ford, if you realize that mutations resulting in "gross morphological
change" most often have severe detrimental effects, what makes you think
anyone can point out 20 of them with beneficial effects?
You have dropped a 500 kilo napalm bomb on a teensy little strawman of your
own construction.
Big deal.
Get this straight- no one thinks that evolution works that way. Your
weaseling about a new enzyme being "a new structure" or not shows you know
it perfectly well- you are just too wedded to some ideology to admit it.
Evolution, in case you missed the last century and a half, works through
miniscule incremental changes. It works through coopting existing
structures into performing new tasks.
And you want to hear a deep, dark secret? One that the EAC, if it existed,
would hunt me down and mind-wipe me for revealing?
You don't even need new structures for speciation to occur.
Isn't that a hoot?
Chris
Tracy Hamilton
That is correct. Because Salisbury was not talking about
beneficial mutations, but variability. My response was talking
about how much more is known about the types of mutations that
lead to much more variability than just point mutations. That addresses
Salisbury's concern. Now it may not address your concern, but
if you can't tell the difference between what Salisbury was talking about
and what you are asking, then more learning on your part is
called for and less quoting of people whose articles you
don't understand, much less old articles that whose questions have
been answered.
Do you think that a single mutation is thought to give rise to morphological
change? That is what your question is framed in terms of. If that were so,
then, that is rather easier to answer. It happens a lot in plants where
doubling or hybridization give novel structures.
There can be significant change with no speciation. cabbage, broccoli,
kohlrabi, cauliflower, and Brussels sprouts are all the same species.
Novel structures, or no?
The Botanical society gives a rather nice explanation of the origin
of wheat grasses, and explains why ID is useless to boot.
http://www.botany.org/newsite/announcements/evolution.php
Please note where they explain that it took years to find all this
out, and this is for rather easy to see mechanisms (drastic
one step changes).
However, most cases of where there is known morphological change, the
details of the genetics is unknown. For example, what is seen
morphologically
is a normal distribution of traits, that segregates into two normal
distributions.
Such as the change in leg length in Anole lizards.
Octopi with suckers that don't work as suckers, but emit light (no crap
about
assuming they are suckers please - they are suckers, but they don't suck)
Andy Groves gave a nice little post "The evolution of morphological
diversity - lecture report "
that details the specific changes that led to changes in morphology in
sticklebacks.
> > It is about all the different
> > kinds of things that lead to significant change. First of all,
> > not all mutations are point mutations.
>
> I knew that.
Then why quote Salisbury in being skeptical of the sufficiency of mutation
as source of variation when he in fact could not have known about many
sources of variation?
> > For example, transposons were
> > not generally realized for how important they are, which is why
> > Barbara McClintock did not get the Nobel prize until 12 years
> > after Salisbury's article.
> >
> > Second, there are genes whose effects on phenotype are major (HOX
> > genes, discovered first 7 years after Salisbury's article), with rather
> > significant differences arising in phenotype just from changing
> > timing or expression quantities, or rather subtle changes.
>
> I was once told that "HOX mutations, as all mutations with
> drastic effects, usually lower survival radically"-- would you
> agree?
I would agree. Is there something about the word "usually" you
don't understand?
[snip]
> Better question: What is meant by a new organ or new
> structure having a new function?
>
> > Is a dog's paw and my hand
> > two of the same thing, or two new structures? Is a new
> > enzyme a new structure - ie is structure only cell
> > morphology? Is a breast a new structure, or just a modified
> > sweat gland?
>
> If a dog with paws transformed into a creature having hands
> in place of paws, I'd say the hands were new structures
> having new functions.
Dog paws ARE hands. That is, not that much different
over a very long period of divergence. They have 5 fingers,
nails at the end of the fingers, tarsals, metatarsals, etc.
I wonder just how much change you think should be seen in real time.
> [TH]"Is a new enzyme a new structure" I'm speaking about
> gross morphological changes.
> About your last question, if a population of creatures having
> sweat glands and no breasts transformed into a population of
> creatures in which a proportion of its sweat glands
> transformed into breasts, I'd say that the breasts were new
> structures having new functions.
Breasts ARE modified sweat glands. Is a gland that produces
milk but has no nipple a breast? Monotremes want to know
if they have to keep their clothes on during the half-time show.
Breast have sebaceous glands, that is nothing new, just what is
secreted. But no, that doesn't count as new morphology.
> > > > Does NeoDarwinism include neutral evolution?
> > >
> > > Yes. And no. "Neo-Darwinism" is rather vague, and can include or not
> > > include [TH]"neutral evolution" depending on who is advancing
> > > neo-Darwinism, when, and how.
> >
> > Since neutral evolution was not generally known *in 1971* by
> > most biologists, the answer would be *no*.
>
> What is the answer today, in 2004?
Since it is "Yes. And no." then whoever uses the term (hint: NOT ME)
needs to make it clear.
Do you think we did not notice that you avoided
discussing the part *above* where you started
"agreeing" with Salisbury?
Do you think your bait and switch of natural selection and limited
mutation insufficient to explain all evolution for natural selection
is dead fools anybody?
???
> > And, is there a difference in the distribution because there
> > is a different rate at which two sequences of letters get
> > generated? No.
>
> Difference in the distribution of what?
Sequences generated. This is about the probability of
getting a functional vs. nonfunctional sequence, right?
Actually, there is something analogous that will raise the
rates of getting intelligible English, if one uses vowels more
commonly, always putting u after q, etc. The reverse is
actually used to predict channel capacity for information
transmission.
> > Is much of a sentence only to make sure that a certain word
> > shows up in a certain position next to another? No.
>
> Is much of a DNA sequence, RNA sequence, or amino acid
> sequence the product of certain nucleotides or amino acids
> having to appear next to certain other nucleotides or amino
> acids?
The question makes no sense. RNA and proteins fold into
3-D structures. Only limited parts are involved in the active site.
> > That you can even entertain such an analogy betrays deep ignorance of
the
> > nature of structure-function relationships in biomolecules.
>
> I had no idea that Hubert Yockey has [TH]"deep ignorance of the
> nature of structure-function relationships in biomolecules."
I didn't see Hubert Yockey making the statements above
about language. I think it much more likely that David Ford
misunderstood Hubert Yockey's arguments.
I note that Yockey does not argue based on analogy to language.
He actually computes things based on certain assumptions, and
hence are relevant to particular abiogenesis scenarios with certain
*assumptions* about what is required.
This is not the first question that should be asked. It is why length
101 and not shorter?
How are they generated? By changes from previous sequences?
If so, then one has a trajectory through a phase space. If not, one jumps
at random. The probability critically depends on these things.
Another question - why amino acids?
How about experiments, since the theoretical
probabilities depends so critically on assumptions.
Would you think an experiment that generated random sequences and selected
for
a specific activity would work? If it was so improbable, there would
be no sequence with the activity to select, and the experiment would
fail.
Are you game for dealing with the *reality* of how often sequences
give rise to a specific chemical activity?
> Same question, this time for amino acid sequences
> of length 202?
> Of length 303?
> Of length 404?
> Of length 505?
> Of length 606?
> Of length 707?
> Of length 808?
> Of length 909?
> Of length 1010?
>
> Also, how long is the biggest functional amino acid sequence
> of which you're aware?; of all possible amino acid sequences
> of that length, what proportion of those sequences will be
> functional proteins of some sort?
It doesn't matter. Huge proteins in general are used by copying rather
large
secondary structures, so a random generation model from individual
amino acids is IRRELEVANT.
[snip]
Gotta go.
Tracy P. Hamilton