Darwinian Mechanism of Mutation and Natural Selection Found Lacking (4)

On Apr 8, 1:05 pm, John Harshman <jharshman.diespam...@xxxxxxxxxxx>
wrote:
paratope.epit...@xxxxxxxxx wrote:
There has always been highly distinguished scientists of impeccable
credentials with no religious motivations, and not bible thumping
hicks, who openly question the theory of evolution.

Have there? And if so, why should we care? This appears to be an
argument from unspecified authority.

Bizarre attempt at agreement.


The first big
problem with evolution is that the fossil record does not honestly
viewed support it, a fact that famous Prof. Steven Jay Gould of
Harvard has described as "the trade secret of paleontology."

You are confused. That's not at all what Gould said. The trade secret
Gould was referring to was stasis in individual species.

"the extreme rarity of transitional forms in the fossil record
persists as the trade secret of paleontology"

http://en.wikiquote.org/wiki/Talk:Stephen_Jay_Gould

Stephen Jay Gould, professor of geology and paleontology at Harvard
University, explains:

The history of most fossil species include two features particularly
inconsistent with gradualism:

1) Stasis - most species exhibit no directional change during their
tenure on earth.

They appear in the fossil record looking much the same as when they
disappear; morphological change is usually limited and directionless;

2) Sudden appearance - in any local area, a species does not arise
gradually by the steady transformation of its ancestors; it appears
all at once and 'fully formed' (Gould, 1977).

Gould honestly admits that the neo-Darwinian synthesis is not
supported by the fossil evidence and "is effectively dead, despite its
persistence as textbook orthodoxy" (Gould, 1980).

Although stasis is the dominant feature of the history of life,
exceptions to the general pattern of stasis can be cited. Examples of
transitional series can be found at lower taxonomic levels. At higher
taxonomic levels, however, transitional sequences range from scarce to
non-existent. Evidence of gradualism between phyla, classes and even
orders is either non-existent or is much disputed. Certainly, no
pervasive pattern of gradualism exists.

George Gaylord Simpson acknowledged this decades ago as he described
the situation in these terms: "This is true of all thirty-two orders
of mammals...The earliest and most primitive known members of every
order already have the basic ordinal characters, and in no case is an
approximately continuous sequence from one order to another known. In
most cases the break is so sharp and the gap so large that the origin
of the order is speculative and much disputed..."

"This regular absence of transitional forms is not confined to
mammals, but is an almost universal phenomenon, as has long been noted
by paleontologists. It is true of almost all classes of animals, both
vertebrate and invertebrate...it is true of the classes, and of the
major animal phyla, and it is apparently also true of analogous
categories of plants "(Simpson, 1944).

The origin of the phyla constitutes an even greater difficulty for
Darwinian theory. In roughly the same period of time it has taken
Darwinian processes to modify the beak of a finch virtually all of the
major body plans appeared explosively at the Precambrian-Cambrian
boundary in what has come to be known as "Biology's Big Bang." The
results of recent research have squeezed the explosion down to a few
million years. (See Kerr, 1993 and Bowring et al, 1993.)

Darwinian evolution predicts the regular presence of transitional
forms. The fossil record reveals their regular absence. It also
reveals a natural phenomenon which until recently was virtually
ignored by paleontologists. That phenomenon is stasis. The tragedy of
Darwinism is that it has impeded the progress of science by turning
the attention of biologists and paleontologists away from the
empirical data and distracting them from developing theories which
explain the pervasive natural phenomenon of stasis.


Evolutionary theory requires transitional forms for current forms.
These supposedly changed by infinitesimal amounts with each generation
as they evolved into the present varieties, so the fossil record
should show these gradual changes.

But it doesn't.

Not true. The fossil record shows a fair number of gradual changes,
among them the ones that Eldredge and Gould described in their original
paper proposing PE, which you obviously have never read. And the reasons
why the record doesn't show all the gradual changes that one could
imagine are probably taphonomic, not evolutionary.

Instead, it shows the sudden emergence of new species out of nowhere,
fully complete with all their characteristics and not changing over
time. It is almost entirely devoid of forms that can plausibly be
identified as intermediates between older and newer ones. This is
popularly known as the "missing link" problem, and it is massively
systematic across different species and time periods.

Wrong. New species (or really, in the fossil record, morphotypes) don't
arise out of nowhere, but associated with quite similar species that
precede them.

What's worse, this problem is getting worse, not better, as more
fossils are discovered, as the new fossils just resemble those already
found and don't fill in the gaps.

This is contrary to my experience. New fossils fill in gaps all the
time. Recently we have Tiktaalik and Microraptor as nice examples.

Darwinian theory attempts to explain the common ancestry of all
species through the gradual transformation of major body plans. This
theory is in opposition to the fossil evidence and the pervasive
patterns of natural history. An estimated 50 to 100 phyla appear
explosively at the base of the Cambrian. Fossil evidence suggesting
their common ancestry is not found in Precambrian rocks. The fossil
data clearly show patterns of stasis rather than of major evolutionary
sequences.

In Darwin's day, it was easy to
claim that the fossils were there but had not been discovered. Problem
is, we now have hundreds of thousands of well-catalogued fossils, from
all continents and geologic eras, and we still haven't found all of
the intermediate forms required to honestly say there is a gradual
transition in forms throughout the fossil record for life forms
present today.

What would "all" mean above? Do you mean we need every intermediate in
order to claim there there are intermediates?

Enter Punctuated Equilibrium:

The usual response of evolutionists the theory of punctuated
equilibrium, Gould's great contribution, which basically says that
evolution occurs not gradually, but in large steps or spurts. This
would explain why there are gaps and not continuity in the fossil
record. Punctuated equilibrium still has no explanation for the large
jumps from one form to another.

Actually, no. You don't know, after all these years, what PE is. Gould
is perhaps partly responsible, because he counters PE with a strawman
theory of "phyletic gradualism". Let's just say that "gradual" in
geological time doesn't mean the same as it does in human experience. A
change occurring over 100,000 years is sudden in geological time.

As Niles Eldredge and Stephen Jay Gould put it: "Stasis is data", "we
must understand that nothing happens most of the time -- and we don't
because our stories don't admit this theme -- if we hope to grasp the
dynamics of evolutionary change. The Burgess Shale teaches us that,
for the history of basic anatomical designs, almost everything
happened in the geological moment just before, and almost nothing in
more than 500 million years since" We need a theory to explain the
phenomenon of stasis and a theory to explain why species do not appear
to gradually evolve into something substantially different.


Computer Technology and Cladistic analysis:

Another development that has undermined evolution is the spread of
computers into evolutionary biology. Computers have shown that when
the characteristics of different living things are encoded in
numerical form and the computer is asked to sort them into sequences
based on their similarities and differences, the computer can find any
number of ways of doing so that have just as much support in the data
as those drawn up by humans to fit an evolutionary tree.

This is word salad applied to phylogenetic analysis. I don't recognize
anything you say here, and phylogenetic analysis is just what I do every
day. In fact, cladistic analysis commonly shows that only one tree is
compatible with the data.

The data can say "no evolution" just as loudly as they say
"evolution"; it's just the pattern-craving human mind that gives
prominence to the former way of viewing it. This is known as phenetic
analysis. When the computer is constrained to push the data into an
evolutionary tree, (this is called cladistic analysis) it tends to
generate trees with all species as individual twigs and no species
forming the crucial lower branches of the tree that evolution demands.
As a result of this, many biologists have in practice stopped using
the idea of ancestors and descendants when classifying new species.
When the British Museum of Natural History did this a few years ago,
they started a small war in scientific circles.

Again, this is so garbled as to be useless. I'll just say that you
understand nothing at all about how phylogenetic analysis is done, or
what the issues are in the field, to the point that I have no idea where
to begin in discussing it with you.

Darwin's said in The Origin of Species, "The geological record is
extremely imperfect and this fact will to a large extent explain why
we do not find intermediate varieties, connecting together all the
extinct and existing forms of life by the finest graduated steps. He
who rejects these views on the nature of the geological record, will
rightly reject my whole theory." 120 years later, hundreds of
billions of fossils and our museums now are filled with over 100
million fossils of 250,000 different species. The availability of this
of hard scientific data should permit us to determine if Darwin was on
the right track.

What is the picture that the fossils have given us? Do they reveal a
continuous progression of all organisms from a common ancestor? With
every geological formation explored and every fossil classified it has
become apparent that these fossils still do not provide the evidence
that Darwin hoped would be forthcoming. The gaps between major groups
of organisms have been growing even wider and more undeniable.

The fossil museums have had to face the gaps in the fossil record and
present new theories of evolution to explain the conflicts between neo-
Darwinian theory and the hard facts of paleontology.

Dr. Niles Eldredge, curator of Invertebrate Paleontology at the
American Museum, collaborated with Dr. Stephen Jay Gould of Harvard,
and calling their new theory to exlain the gaps punctuated
equilibria.

Dr. David Raup, curator of geology at the Field Museum of Natural
History in Chicago, published an article in the January 1979 issue of
the museum's journal entitled "Conflicts Between Darwinism and
Paleontology" in which he stated that the 250,000 species of plants
and animals recorded and deposited in museums throughout the world did
not support the gradual unfolding hoped for by Darwin.

The following April, Dr. Colin Patterson, a senior paleontologist and
editor of a prestigious journal at the British Museum of Natural
History, wrote in a letter to the author that he didn't know of any
real evidence of evolutionary transitions either among living or
fossilized organisms.

"One of the reasons I started taking this anti-evolutionary view,
was ... it struck me that I had been working on this stuff for twenty
years and there was not one thing I knew about it. That's quite a
shock to learn that one can be so misled so long. ...so for the last
few weeks I've tried putting a simple question to various people and
groups of people. Question is: Can you tell me anything you know about
evolution, any one thing that is true? I tried that question on the
geology staff at the Field Museum of Natural History and the only
answer I got was silence. I tried it on the members of the
Evolutionary Morphology Seminar in the University of Chicago, a very
prestigious body of evolutionists, and all I got there was silence for
a long time and eventually one person said, 'I do know one thing -- it
ought not to be taught in high school'."
Dr. Colin Patterson, Senior Paleontologist, British Museum of
Natural History, London Keynote address at the American Museum of
Natural History, New York City, 5 November, 1981

"It is easy enough to make up stories of how one form gave rise to
another, and to find reasons why the stages should be favored by
natural selection. But such stories are not part of science, for there
is no way of putting them to the test." Personal letter (written 10
April 1979) from Dr Collin Patterson, Senior Paleontologist at the
British Museum of Natural History in London, to Luther D. Sunderland;
as quoted in Darwin's Enigma by Luther D. Sunderland, Master Books,
San Diego, USA, 1984, p. 89.


Enter the Lungfish:

Evolution also suffers from the problem that many sequences which look
logical based on the progression of one set of anatomical
characteristics suddenly look illogical when attention is switched to
another set. For example, the lungfish superficially seems to make a
good intermediate between fish and amphibian, until one examines the
rest of its internal organs, which are not intermediate in character,
nor are the ways in which its eggs develop.

Of course modern lungfish are only intermediate in a few ways, those
being the retained characteristics they share with the common ancestor.
Another strawman.

Phylogenetic Analysis of DNA Sequences

The emergence of one species from another has never been directly
observed by science.

Actually, not true. See Coyne and Orr.

Disagree here. This is still true and not directly observed by Coyne
or Orr in Drosphila. Two books focused on species: Theodosius
Dobzhansky's Genetics and the Origin of Species, and Ernst Mayr's
Systematics and the Origin of Species. Jerry Coyne and Allen Orr's new
book, Speciation, inspired by Dobzhansky's. Coyne and Orr largely
ignore the work of those who actually identify, delimit and describe
species.


Phylogenetic analysis based on computer analysis
of DNA sequencing is not direct observation of one species emerging
from another, and is not proof of speciation because it ignores the
time limitations of the reproductive cycle of the organism. For the
mutational changes to occur randomly and then to be selected by
survival advantage requires many reproductive cycles which is feasible
in rapidly reproducing viruses and bacteria, but becomes problematic
in higher animals which have reproductive cycles in years instead of
days.

This appears to be a non sequitur. Actually, observed (or inferred from
phylogeny, if you prefer) substution rates are entirely compatible with
those expected based on length of reproductive cycles. And if they
weren't, this would not be evidence against speciation anyway.

False. This obviously would be evidence against the theory of
speciation based on random mutations selected by survival advantage.

Nor does
it seem to have anything to do with phylogenetic analysis of DNA sequences.

Wrong again.


Enter Molecular Biology:

More difficult to explain are complex chemical reactions and molecular
structures that living things are made of. There are no plausible
accounts of how they could have evolved from other simpler processes
because as one hypothesizes back down the hypothetical chain of
complexity, one comes to a point at which the process simply won't
work if it gets any simpler.
At this stage, the process couldn't have evolved from anything else
because there is nothing simpler for it to have evolved from. And at
this stage, the process is still far too complex to have been thrown
together by any known non-living chemical event. At one time,
knowledge of the complex processes of living things was limited
enough, and hopes for the discovery of intermediate processes that
they could have evolved from wide-open enough, that evolutionists
could ignore this problem. But as biological research has progressed,
this gap too has been filled with more and more inconvenient facts. As
in the case of the other problems challenging evolution, the key thing
here is the intellectual direction: research is consistently making
the problem worse, not better.http://www.charliewagner.net/

Another similar example:

What do you mean "another"? So far you have presented no examples, just
handwaving. "It's too complex so it couldn't have evolved", and that's
the whole of your argument, if it can be so dignified.

one of the things that has happened since
evolution was first proposed is that biology has found thousands of
different proteins that make up organisms. It was hoped that a
thorough cross-species comparison of these would reveal the kinds of
relationships of graded similarity that evolution implies. But it
hasn't. Instead, it has given the same picture of distinct species
that examination of gross anatomy does. It's the same old story of a
tree with all twigs and no branches!http://www.charliewagner.net/

This is hardly true. There are families of proteins, and the families
are ordered into families themselves. The processes that produce new
proteins are quite well understood.

Wishful thinking.


Analysis of the closeness and distance between different species
reveals bizarre results. For example, according to the sequence
difference matrix of vertebrate hemoglobins in the standard Dayhoff
Atlas of Protein Structure and Function, man is as close to a lamprey
as are fish! This problem repeats itself with other characteristics of
organisms.

This is Denton's fallacy, which he himself has abandoned, though you
have not. You understand that this particular pattern of similarity is
exactly as expected under a molecular clock, right?

Concept of molecular clock is still very controversial. Because clock
rate changes based on various paramenters. Causing evolution of
proteins at differing rates. See: How Valid is the Molecular Clock
Hypothesis? "The validity of a molecular clock, except in closely
related species, still remains controversial." Extrapolating across
wide biological distances, such as from fish to other vertebrates,
that is controversial.

The idea of the molecular clock hypothesis was first proposed by Emile
Zuckerkandl and Linus Pauling. Gillooly, et al, published in the
Proceedings in the National Academy of Sciences, entitled The Rate of
DNA Evolution, Effects of Body Size and Temperature on the Molecular
Clock. In this publication, they say that, in fact, the size of an
organism and temperature can affect how fast or how slow this clock
might tick. Francisco Ayala wrote Vagaries of the Molecular Clock.
Tomoka Ohta: An Examination of the Generation-time Effect on Molecular
Evolution ( generation-time effect). Drummond, Why Highly Expressed
Proteins Evolve Slowly.


Enter Abiogenesis

Another problem with evolution that has only gotten worse with
increasing biological knowledge is the question of how life initially
emerged from dead matter. The simplest possible cell imaginable
within the limits of biology, let alone the simplest actually existing
cell, is far too complex to have been thrown together by any known non-
living chemical event. So even if evolution has an explanation of how
species evolve from one to another, it has no way to "get the ball
rolling" by producing the first species from something that is not a
species.

Not my department. I will merely point out that it hardly invalidates
theories of subsequent evolution even if we don't know how the first
cell arose.

Ignorance is bliss.


Evolution Not Even Science After All

Many such as Karl Popper, for example, have questioned whether
evolution is a science at all, because its assertions are not
potentially falsifiable.

No, Popper never said any such thing. You are confused about what Popper
said, and he later retracted the claim he actually did make.

Popper proposed his famous criterion of falsification to solve the
demarcation problem: good science is done when hypotheses can be shown
to be false (if they indeed are). Popper understood evolutionary
biologists to say that their theory predicts that natural selection
allows only the fittest organisms to survive; but, he countered, the
"fittest" organisms are defined as those who survive, which makes the
statement tautological. Popper initially concluded that, though
tautological, evolutionary theory was a useful program, i.e., an idea
that could provide a powerful framework to interpret the biological
world. But, as in the case of Freudian psychoanalysis or Marxist
history, it wasn't good science.

Why, then, did the Austrian philosopher recant and change his mind?
Because it turns out that certain aspects of natural selection involve
predictions which can be considered falsifiable. Predictions about
population traits in response to environmental pressures are
falsifiable hypothesis, in the same sense in which other science
predictions are made, and very much unlike the explanations of human
behavior put forth by psychoanalysts, which can fit virtually any
observed pattern. However, in aspects of evolutionary theory which
are non-falsifiable, Popper would stand by his position and claim non-
falsifiable tautology is pseudoscience same as
Freudian psychoanalysis or Marxian history. And guess what? Colin
Patterson says evolution is not testable:"It is easy enough to make up
stories of how one form gave rise to another, and to find reasons why
the stages should be favored by natural selection. But such stories
are not part of science, for there is no way of putting them to the
test." Personal letter (written 10 April 1979) from Dr Collin
Patterson to Luther D. Sunderland; as quoted in Darwin's Enigma by
Luther D. Sunderland. Therefore, Karl Popper's initial reasoning is
still vaild. Evolution is pseudoscience.


A true science, like physics, makes claims
that can be tested and thus potentially falsified; this vulnerability
is what makes it worthy of belief when despite this, the falsification
does not happen. But evolution does not make claims of this kind.
Science is based on repeatable experiments. The data used to support
evolution are neither experiments nor repeatable, nor can they be,
since the origin of species on earth was a unique event.

This is exactly the sort of ignorance about how science actually works
that Popper would never have been guilty of.

Perhaps you can explain the design of an experiment which shows how
the origin of the species can be falsified. Perhaps you can do what
Colin Patterson could not. If you cannot, then simply admit it.


Evolution
isn't even science, it's a simply smelly garbage that is left over
from the last party before the cleaning people show up.http://www.charliewagner.net/

You claim not to be a creationist, yet you seem to get all your
information and arguments from creationist web sites. Odd.

Typical statement of fact based on zero knowledge.

Is this Charlie Wagner, or is it someone plagiarizing Charlie Wagner?


Many questions, few answers.


It is constantly a source of wonder and amazement to me that highly
competent scientists, whom I otherwise hold in high regard, have not
come to these same conclusions. The conclusions are that life could
not have arisen de novo on a barren earth, and that all of the life
forms that we see today could not have appeared as a result of the
darwinian mechanism of mutation and natural selection.

The evidence for evolution is broken down into three broad
catagories.

The first is direct evidence of small-scale changes in controlled
laboratory experiments.

The second is direct evidence based upon sequences in the fossil
record.

The third is the vestigial argument, the idea that the signs of
history are preserved within every organism which record pathways of
historical descent.

You seem to have left out a number of broad categories. But let's stick
with these for now.

I have never denied for a moment that mutations occur, or that natural
selection occurs. What I'm saying is that it is a trivial effect, with
no creative power to produce new forms. Evolution correctly is defined
as a change in the frequency of genes in a population. The leap of
faith, which I refuse to take, is that these changes can accumulate to
the point where new species, genera and classes are formed. Artificial
selection experiments in laboratories have demonstrated that there is
a point beyond which you cannot go. Why should it be any different in
nature?

I missed those experiments. Where do I find them?


Look it up. Try Google.

Let's start at the beginning. Could life have arisen de novo on the
primitive earth? I won't rule it out, but I consider it very unlikely
given what we know. It is becoming more clear as time goes on, that
the primitive atmosphere contained little, if any, ammonia, methane
and hydrogen. This puts all of the experiments of Fox and Miller in
question. A much more likely scenario, is that the primitive
atmosphere was rich in carbon dioxide, nitrogen and water vapor. No
one to my knowledge, has proposed any believable mechanism that would
cause these perfectly stable molecules to combine together into RNA,
DNA, proteins, cells, tissues and organisms. You can't even get past
the first step. In addition, the oldest cells date back to around 3.45
billion years old. The earth probably only became habitable for life
at around 3.8 billion years ago. This leaves you with only 350 million
years for the processes of photosynthesis, replication, cell
respiration and all of the enzymes needed by these processes to
evolve. I just don't think that's enough time.

What do you think happened? It seems much more likely to me that life
came to earth from elsewhere, with all of these processes already in
place. I think the key to it all is the water. The earth appears t o
be the only planet in the solar system with large quantities of water,
which is necessary for life to flourish

There seems to be less evidence for your conjecture than for the
standard one. There are big problems with moving life around the
universe, chiefly radiation, vacuum, and time.

That's all well and good, but it only postpones the question.
Where did the space life come from?

Well, now you've come to the question of primary cause. Stated another
way, we may well ask "why is there anything, instead of nothing?" At
some point in time, you've got to get to something that has always
existed. Conventional thinking calls this something God. But it may
just as well be the universe as God, in my mind. We must consider the
possibility that the universe, and the life in it have always existed.
It may just be that the question "why is there life?" is no different
from the question "why is there matter?"

One problem here is that the universe has not always existed, so life
can't have always existed in it. There has to be a beginning, unless you
are positing that life can be transferred between universes and so
arrived here from somewhere else.

Getting back to evolution, scientists claim that there is a "mountain
of evidence" for evolution.
Do you deny this?

Well, I just don't see it. There is a "mountain of evidence" that all
living forms are related. Of that there can be no doubt. In fact, this
relatedness is profound. I think this is the evidence that they are
talking about. The similarities in genes found across the spectrum of
living things is astounding. The same genes are present in all kinds
of animals, and even in plants. There is a gene in the bean plant that
codes for hemoglobin, which is never used by a bean plant. Why is it
there?

Actually, it *is* used.

Sure, beans have red blood cells just like the tooth fairy.


But this profound relatedness, does not mean that one organism
is ancestral or descendant to another.

As usual, it's impossible to determine what you actually mean by
"related". If it doesn't mean ancestry and descent, what does it mean?
What alternative phenomenon to ancestry and descent are you postulating
under the name "related"? Until we know, we can't determine if your
theory even makes sense, much less fits the data.

What do you think it means?


And furthermore, this
relatedness says nothing about the mechanism by which these forms
appeared, certainly it does not support the mechanism of mutation and
natural selection.

Agreed.

paratope.epitope

.

Relevant Pages

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